Speeding-up the Determination of Protein-Ligand Affinities by STD NMR: The Reduced Data Set STD NMR Approach (rd-STD NMR).

STD NMR spectroscopy is a powerful ligand-observed NMR tool for screening and characterizing the interactions of small molecules and low molecular weight fragments with a given macromolecule, identifying the main intermolecular contacts in the bound state. It is also a powerful analytical technique for the accurate determination of protein-ligand dissociation constants (KD) of medium-to-weak affinity, of interest in the pharmaceutical industry. However, accurate KD determination and epitope mapping requires a long series of experiments at increasing saturation times to carry out a full analysis using the so-called STD NMR build-up curve approach and apply the "initial slopes approximation". Here, we have developed a new protocol to bypass this important limitation, which allows us to obtain initial slopes by using just two saturation times and, hence, to very quickly determine precise protein-ligand dissociation constants by STD NMR.

The taxonomy of Sahelanthropus tchadensis from a craniometric perspective.

Sahelanthropus tchadensis has raised much debate since its initial discovery in Chad in 2001, given its controversial classification as the earliest representative of the hominin lineage. This debate extends beyond the phylogenetic position of the species, and includes several aspects of its habitual behavior, especially in what regards its locomotion. The combination of ancestral and derived traits observed in the fossils associated with the species has been used to defend different hypotheses related to its relationship to hominins. Here, the cranial morphology of Sahelanthropus tchadensis was assessed through 16 linear craniometric measurements, and compared to great apes and hominins through Principal Component Analysis based on size and shape and shape information alone. The results show that S. tchadensis share stronger morphological affinities with hominins than with apes for both the analysis that include size information and the one that evaluates shape alone. Since TM 266-01-060-1 shows a strong morphological affinity with the remaining hominins represented in the analysis, our results support the initial interpretations that S. tchadensis represents an early specimen of our lineage or a stem basal lineage more closely related to hominins than to Panini.

Theories of Relativistic Dissipative Fluid Dynamics.

Relativistic dissipative fluid dynamics finds widespread applications in high-energy nuclear physics and astrophysics. However, formulating a causal and stable theory of relativistic dissipative fluid dynamics is far from trivial; efforts to accomplish this reach back more than 50 years. In this review, we give an overview of the field and attempt a comparative assessment of (at least most of) the theories for relativistic dissipative fluid dynamics proposed until today and used in applications.

Antimicrobial Resistance Profiles of Multidrug-Resistant Enterobacteria Isolated from Feces of Weaned Piglets.

Nosocomial infections caused by multidrug-resistant enterobacteria have become a major challenge in global public health. Previous studies have indicated that use of antibiotics in livestock production chains is linked to the rising threat of antibiotic resistance in humans. In this study, we aimed to evaluate the distribution of genes encoding resistance to tetracycline, ß-lactams, and colistin in multidrug-resistant enterobacteria isolated from feces of weaned pigs. Ninety-four enterobacteria isolates were submitted to antibiotic susceptibility test by minimum inhibitory concentration (MIC). In addition, we performed conjugation experiments to verify if plasmid-bearing isolates containing the mcr-1 gene could transfer their resistance determinant to a colistin-sensitive recipient strain. Our results demonstrated a positive association between the detection of antibiotic resistance genes in enterobacteria and the phenotypic resistance profiles of the bacterial isolates. At least one of the extended-spectrum ß-lactamases (ESBL) genes (blaCTX-M, blaTEM, or bla SHV) and tetA was found among most bacterial genera analyzed. In addition, results revealed that the mcr-1 gene can be transferred from E. coli UFV-627 isolate to an F- recipient (Escherichia coli K12) by conjugation. Our findings support the hypothesis that swine represents an important reservoir of antibiotic resistance genes and suggest that horizontal transfer mechanisms (e.g., conjugation) may mediate the spread of these genes in the swine gastrointestinal tract.

Ledi-Geraru strikes again: Morphological affinities of the LD 350-1 mandible with early Homo.

The origins of the genus Homo have been a focus of much debate in the paleoanthropological literature due to its importance in understanding the evolutionary trajectories that led to the appearance of archaic humans and our species. On the level of taxonomic classification, the controversies surrounding the origins of Homo are the result of lack of clear classification criteria that separate our genus from australopiths, given the general similarities observed between fossils ascribed to late australopiths and early Homo. The challenge in finding clear autapomorphies for Homo has even led to debates about the classification of Homo habilis and Homo rudolfensis as part of our genus. These debates are further complicated by the scarcity of fossils in the timeframe of appearance of our genus, making any fossils dated to between 3.0 and 2.5 Ma of particular relevance in the context of this discussion. The Ledi-Geraru mandible is one such fossils, which has called the attention of researchers due to its combination of primitive traits seen in Australopithecus and derived traits observed in later Homo. Despite being fragmented and poorly preserved, it is one of the key fossil specimens available from the period mentioned above.

Selection of Multidrug-Resistant Enterobacteria in Weaned Pigs and Its Association With In-feed Subtherapeutic Combination of Colistin and Tylosin.

In-feed antibiotics are administered to piglets to improve performance and production efficiency. However, the use of growth promoters in the swine industry can select for multidrug-resistant (MDR) bacteria. Here, we evaluate the resistance profile of enterobacteria isolated from fecal samples of weaned pigs (21-35 days) fed or not with antibiotics (colistin and tylosin) and investigated the piglets gut microbiota in both groups. Six hundred and eighteen bacterial cultures were isolated from the control group (CON; n = 384) and antibiotic-fed pigs (ATB; n = 234). All isolates were tested for resistance to 12 antibiotics belonging to six distinct antibiotic classes. Isolates were highly resistant to ampicillin (90%; n = 553), amoxicillin (85%; n = 525), and tetracycline (81%; n = 498). A significant increase (P < 0.05) in resistance to cephalexin, kanamycin, doxycycline, and colistin was observed for bacteria from the ATB group. Piglets allocated in the ATB and CON groups shared similar intestinal microbiota, as revealed by alpha- and beta-diversity analyses. Our findings demonstrate that colistin and tylosin contribute to select MDR enterobacteria in weaned piglets. The high frequency of antibiotic resistance among isolates from the CON group suggests that environmental sources (e.g., fecal contents, aerosols, soil, water, food) also represent a potential reservoir of multidrug-resistant enterobacteria in pig production systems.

Novel Relaxation Time Approximation to the Relativistic Boltzmann Equation.

We show that the widely used relaxation time approximation to the relativistic Boltzmann equation contains basic flaws, being incompatible with micro- and macroscopic conservation laws if the relaxation time depends on energy or general matching conditions are applied. We propose a new approximation that fixes such fundamental issues and maintains the basic properties of the linearized Boltzmann collision operator. We show how this correction affects transport coefficients, such as the bulk viscosity and particle diffusion.

miR156-targeted SPL10 controls Arabidopsis root meristem activity and root-derived de novo shoot regeneration via cytokinin responses.

Root growth is modulated by different factors, including phytohormones, transcription factors, and microRNAs (miRNAs). MicroRNA156 and its targets, the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, define an age-dependent pathway that controls several developmental processes, including lateral root emergence. However, it remains unclear whether miR156-regulated SPLs control root meristem activity and root-derived de novo shoot regeneration. Here, we show that MIR156 and SPL genes have opposing expression patterns during the progression of primary root (PR) growth in Arabidopsis, suggesting that age cues may modulate root development. Plants with high miR156 levels display reduced meristem size, resulting in shorter primary root (PRs). Conversely, plants with reduced miR156 levels show higher meristem activity. Importantly, loss of function of SPL10 decreases meristem activity, while SPL10 de-repression increases it. Meristem activity is regulated by SPL10 probably through the reduction of cytokinin responses, via the modulation of type-B ARABIDOPSIS RESPONSE REGULATOR1(ARR1) expression. We also show that SPL10 de-repression in the PRs abolishes de novo shoot regenerative capacity by attenuating cytokinin responses. Our results reveal a cooperative regulation of root meristem activity and root-derived de novo shoot regeneration by integrating age cues with cytokinin responses via miR156-targeted SPL10.

Evaluation of methods for the quantification of ether extract contents in forage and cattle feces.

The objective of this study was to compare the estimates of ether extract (EE) contents obtained by the Randall method and by the high-temperature method of the American Oil Chemist's Society (AOCS; Am 5-04) in forages (n = 20) and cattle feces (n = 15). The EE contents were quantified by using the Randall extraction or AOCS method and XT4 filter bags or cartridges made of qualitative filter paper (80 g/m²) as containers for the samples. It was also evaluated the loss of particles, and concentration of residual chlorophyll after extraction and the recovery of protein and minerals in the material subjected to extraction. Significant interaction was observed between extraction method and material for EE contents. The EE estimates using the AOCS method were higher, mainly in forages. No loss of particles was observed with different containers. The chlorophyll contents in the residues of cattle feces were not affected by the extraction method; however, residual chlorophyll was lower using the AOCS method in forages. There was complete recovery of the protein and ash after extraction. The results suggest that AOCS method produces higher estimates of EE contents in forages and cattle feces, possibly by providing greater extraction of non-fatty EE.

Evaluation of Laboratory Procedures to Quantify the Neutral Detergent Fiber Content in Forage, Concentrate, and Ruminant Feces.

A comparison was made of measurements of neutral detergent fiber concentrations obtained with AOAC Method 2002.04 and modified methods using pressurized environments or direct use of industrial heat-stable α-amylase in samples of forage (n=37), concentrate (n=30), and ruminant feces (n=39). The following method modifications were tested: AOAC Method 2002.04 with replacement of the reflux apparatus with an autoclave or Ankom(220®) extractor and F57 filter bags, and AOAC Method 2002.04 with replacement of the standardization procedures for α-amylase by a single addition of industrial α-amylase [250 µL of Termamyl 2X 240 Kilo Novo Units (KNU)-T/g] prior to heating the neutral detergent solution. For the feces and forage samples, the results obtained with the modified methods with an autoclave or modification of α-amylase use were similar to those obtained using AOAC Method 2002.04, but the use of the Ankom220 extractor resulted in overestimated values. For the concentrate samples, the modified methods using an autoclave or Ankom220 extractor resulted in positive systematic errors. However, the method using industrial α-amylase resulted in systematic error and slope bias despite that the obtained values were close to those obtained with AOAC Method 2002.04.

Lysine requirement for growing-finishing immunocastrated male pigs.

Eighty boars (19.3 ± 2.49 kg) were vaccinated twice (100 and 128 days of age) against gonadotropin releasing hormone (Vivax™ vaccine), for a randomised block design study aiming to evaluate five digestible lysine (DLys) level treatments, with three phase-feeding per treatments (9-8-7; 10-9-8; 11-10-9; 12-11-10 and 13-12-11 g/kg) during the growing-finishing phases (54-100, 100-128 and 128-155 days of age, respectively). Pigs were fed their respective diets ad libitum from 54 to 155 days and weighed at 100, 128 and 155 days. Pig loin (Longissimus dorsi) area, loin depth and backfat thickness were measured by ultrasound at 100 and 155 days. Hot carcass weight, meat quantity and meat yield were measured at slaughter. From 54 to 100 days (pre-immunocastration), DLys levels linearly improved pig feed conversion and loin area, the level of DLys for minimum feed conversion and maximum loin area was 13 g/kg. However, DLys levels had no effect on the performance of boars from 54 to 128 days (pre-immunocastration), nor on the performance and carcass parameters of immunocastrated male pigs between 54 and 155 days. A sequence of diets containing 9, 8 and 7 g/kg of DLys fed from 54 to 100, 100 to 128 and 128 to 155 days, respectively, meet the requirement of growing-finishing immunocastrated male pigs.

Practical but Inaccurate? A-Mode Ultrasound and Bioelectrical Impedance Underestimate Body Fat Percentage Compared to Dual-Energy X-ray Absorptiometry in Male College Students.

Bioelectrical impedance (BIA) and ultrasound (US) have become popular for estimating body fat percentage (BF%) due to their low cost and clinical convenience. However, the agreement of these devices with the gold-standard method still requires investigation. The aim was to analyze the agreement between a gold-standard %BF assessment method with BIA and US devices. Twenty-three men (aged 30.1 ± 7.7 years, weighing 82.5 ± 14.9 kg, 1.77 ± 0.05 m tall) underwent dual-energy X-ray absorptiometry (DXA), BIA (tetrapolar) and US (three-site method) %BF assessments. Pearson and concordance correlations were analyzed. A T-test was used to compare the means of the methods, and Bland-Altman plots analyzed agreement and proportional bias. Alpha was set at <0.05. The Pearson coefficients of BIA and US with DXA were high (BIA = 0.94; US = 0.89; both p < 0.001). The concordance coefficient was high for BIA (0.80) and moderate for US (0.49). The BF% measured by BIA (24.5 ± 7.5) and US (19.4 ± 7.0) was on average 4.4% and 9.6% lower than DXA (29.0 + 8.5%), respectively (p < 0.001). Lower and upper agreement limits between DXA and BIA were -1.45 and 10.31, while between DXA and US, they were 2.01 and 17.14, respectively. There was a tendency of both BIA (p = 0.09) and US (p = 0.057) to present proportional bias and underestimate BF%. Despite the correlation, the mean differences between the methods were significant, and the agreement limits were very wide. This indicates that BIA and US, as measured in this study, have limited potential to accurately measure %BF compared to DXA, especially in individuals with higher body fat.

Autolyzed yeast and sodium butyrate supplemented alone to diets promoted improvements in performance, intestinal health and nutrient transporter in weaned piglets.

This study investigated the effects of supplemental nucleotides, autolyzed yeast (Saccharomyces cerevisiae), and sodium butyrate in diets for nursery pigs on growth performance, diarrhea incidence, blood profile, intestinal morphology, mRNA expression of nutrient transporters, inflammatory markers, antioxidant profile, and tight junction proteins in the small intestine. One hundred eighty 21-day-old pigs (5.17 ± 0.57 kg) were assigned in a randomized block design to 1 of 4 dietary treatments: (1) CON: control, basal diet, (2) NUC: CON + nucleotides, (3) YSC: CON + lysed yeast S. cerevisiae, (4) ASB: CON + acidifier sodium butyrate. Pigs were fed for 24 days, phase 1 (21-32 days) and 2 (32-45 days). During phase 1, YSC and ASB improved average daily gain (ADG) and feed conversion (FC) compared with CON. At the overall period, ASB improved ADG and YSC improved FC compared with CON. The NUC diet did not affect growth performance. The ASB increased ileal villus height compared to CON. The YSC and ASB reduced the number of Peyer's patches in the ileum compared with CON. The YSC increased mRNA expression of nutrient transporters (SMCT2, MCT1, and PepT1), tight junction proteins (OCL and ZO-1), antioxidants (GPX), and IL1-ß in the jejunum compared with CON. The ASB increased mRNA expression of nutrient transporters (SGLT1 and MCT1), tight junction proteins (OCL and ZO-1), and antioxidants (GPX and SOD) compared with CON. In conclusion, autolyzed yeast and sodium butyrate promoted growth performance by improving the integrity of the intestinal barrier, the mRNA expression of nutrient transporters, and antioxidant enzymes in the jejunum of nursery pigs whereas supplementation of nucleotides did not show such effects.

Carbohydrases and Phytase in Poultry and Pig Nutrition: A Review beyond the Nutrients and Energy Matrix.

This review aimed to clarify the mechanisms through which exogenous enzymes (carbohydrases and phytase) influence intestinal health, as well as their effects on the nutrients and energy matrix in diets fed to poultry and pigs reared under sanitary challenging conditions. Enzyme supplementation can positively affect intestinal microbiota, immune system, and enhance antioxidant status. Although enzymes have been shown to save energy and nutrients, their responses under sanitary challenging conditions are poorly documented. Immune system activation alters nutrient partitioning, which can affect the matrix values for exogenous enzymes on commercial farms. Notably, the carbohydrases and phytase supplementation under sanitary challenging conditions align with energy and nutritional valorization matrices. Studies conducted under commercial conditions have shown that matrices containing carbohydrases and phytase can maintain growth performance and health in poultry and pigs. However, these studies have predominantly focused on assessing a single level of reduction in energy and/or available phosphorus and total calcium, limiting our ability to quantify potential energy and nutrient savings in the diet. Future research should delve deeper into determining the extent of energy and nutrient savings and understanding the effects of alone or blended enzymes supplementation to achieve more specific insights.

Synthesis of multi-layer graphene oxide from HCl-treated coke and Brazilian coals by sulfuric acid thermal exfoliation and ozone oxidation.

This study involved the synthesis and characterization of graphene oxide (GO) from mineral coke and bituminous coal. HCl treated and non-HCl treated ultrafine powder obtained from both precursors were treated with H2SO4, followed by thermal treatment, and oxidation with ozone and ultra-sonication for GO production. The synthesized materials were characterized using Fourier transform infrared spectroscopy (FTIR), zeta potential (ZP), particle size distribution (PSD), transmission electron microscopy (TEM), X-ray diffraction (XRD) and Raman spectroscopy. The results confirmed the exfoliation of the material primarily at the edges of its structure and the formation of multilayer graphene oxide (GO) from mineral coke and bituminous coal. Furthermore, it was found that carbonaceous materials with graphitic morphology are easier to exfoliate and oxidize, leading to the production of higher quality graphene oxide. Therefore, the GO synthesized from mineral coke exhibited the best quality in this study. The methodology used proposes an innovative approach, offering a faster, more economical, and environmentally friendly synthesis compared to the traditional Hummers' method, thereby adding value to other raw materials that can be utilized in this process, such as Brazilian coke and coal.

Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy.

Low-affinity protein-ligand interactions are important for many biological processes, including cell communication, signal transduction, and immune responses. Structural characterization of these complexes is also critical for the development of new drugs through fragment-based drug discovery (FBDD), but it is challenging due to the low affinity of fragments for the binding site. Saturation transfer difference (STD) NMR spectroscopy has revolutionized the study of low-affinity receptor-ligand interactions enabling binding detection and structural characterization. Comparison of relaxation and exchange matrix calculations with 1H STD NMR experimental data is essential for the validation of 3D structures of protein-ligand complexes. In this work, we present a new approach based on the calculation of a reduced relaxation matrix, in combination with funnel metadynamics MD simulations, that allows a very fast generation of experimentally STD-NMR-validated 3D structures of low-affinity protein-ligand complexes.

Intestinal microbial diversity of swines fed with different sources of lithium.

A drug that is widely used in the treatment of psychiatric disorder is lithium (Li) salts. The people who make therapeutic use of this drug develop a series of side effects. Through metataxonomic data, this study assessed the impacts of lithium, as Li carbonate or Li-enriched mushrooms, on the microbial composition of the ileum, colon, and feces of piglets. Employing Bray-Curtis metric, no differences were observed among the treatments evaluated. Nevertheless, the alpha diversity indices showed differences in the Simpson, Shannon, and Chao-1 indices in the colon and Chao-1 in the feces in the diets with Li compared with the diets without Li. The taxa with the highest relative abundance varied among the ileum, colon, and feces, with a predominance of the phyla Firmicutes, Bacteroidota, and Proteobacteria in diets with Li. Many groups of microorganisms that are important for the health of the host (e.g., Lactobacillus, Ruminococcaceae, Enterorhabdus, Muribaculaceae, and Coprococcus) had their relative abundance increased in animals that received diets with the recommended dose of lithium. Furthermore, there was an increase in the abundance of Prevotellaceae and Bacteroidales (in the diet with Li-enriched mushroom) and Clostridia, Ruminococcus, Burkholderia, and Bacteroidales (diets with Li carbonate) at the recommended dosages. This is the first study to show the effects of Li carbonate and Li-enriched mushrooms on the intestinal microbiota of piglets. Thus, the effects of lithium on the body may be related to its ability to change the composition of the intestinal microbiota. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-03938-3.

New avenues for the treatment of immunotherapy-resistant pancreatic cancer.

Pancreatic cancer (PC) is characterized by its extremely aggressive nature and ranks 14th in the number of new cancer cases worldwide. However, due to its complexity, it ranks 7th in the list of the most lethal cancers worldwide. The pathogenesis of PC involves several complex processes, including familial genetic factors associated with risk factors such as obesity, diabetes mellitus, chronic pancreatitis, and smoking. Mutations in genes such as KRAS, TP53, and SMAD4 are linked to the appearance of malignant cells that generate pancreatic lesions and, consequently, cancer. In this context, some therapies are used for PC, one of which is immunotherapy, which is extremely promising in various other types of cancer but has shown little response in the treatment of PC due to various resistance mechanisms that contribute to a drop in immunotherapy efficiency. It is therefore clear that the tumor microenvironment (TME) has a huge impact on the resistance process, since cellular and non-cellular elements create an immunosuppressive environment, characterized by a dense desmoplastic stroma with cancer-associated fibroblasts, pancreatic stellate cells, extracellular matrix, and immunosuppressive cells. Linked to this are genetic mutations in TP53 and immunosuppressive factors that act on T cells, resulting in a shortage of CD8+ T cells and limited expression of activation markers such as interferon-gamma. In this way, finding new strategies that make it possible to manipulate resistance mechanisms is necessary. Thus, techniques such as the use of TME modulators that block receptors and stromal molecules that generate resistance, the use of genetic manipulation in specific regions, such as microRNAs, the modulation of extrinsic and intrinsic factors associated with T cells, and, above all, therapeutic models that combine these modulation techniques constitute the promising future of PC therapy. Thus, this study aims to elucidate the main mechanisms of resistance to immunotherapy in PC and new ways of manipulating this process, resulting in a more efficient therapy for cancer patients and, consequently, a reduction in the lethality of this aggressive cancer.

Immune pathway through endometriosis to ovarian cancer.

Endometriosis is an estrogen-dependent inflammatory disease, defined by the presence of functional endometrial tissue outside of the uterine cavity. This disease is one of the main gynecological diseases, affecting around 10%-15% women and girls of reproductive age, being a common gynecologic disorder. Although endometriosis is a benign disease, it shares several characteristics with invasive cancer. Studies support that it has been linked with an increased chance of developing endometrial ovarian cancer, representing an earlier stage of neoplastic processes. This is particularly true for women with clear cell carcinoma, low-grade serous carcinoma and endometrioid. However, the carcinogenic pathways between both pathologies remain poorly understood. Current studies suggest a connection between endometriosis and endometriosis-associated ovarian cancers (EAOCs) via pathways associated with oxidative stress, inflammation, and hyperestrogenism. This article aims to review current data on the molecular events linked to the development of EAOCs from endometriosis, specifically focusing on the complex relationship between the immune response to endometriosis and cancer, including the molecular mechanisms and their ramifications. Examining recent developments in immunotherapy and their potential to boost the effectiveness of future treatments.

The neurobiological effects of senescence on dopaminergic system: A comprehensive review.

Over time, the body undergoes a natural, multifactorial, and ongoing process named senescence, which induces changes at the molecular, cellular, and micro-anatomical levels in many body systems. The brain, being a highly complex organ, is particularly affected by this process, potentially impairing its numerous functions. The brain relies on chemical messengers known as neurotransmitters to function properly, with dopamine being one of the most crucial. This catecholamine is responsible for a broad range of critical roles in the central nervous system, including movement, learning, cognition, motivation, emotion, reward, hormonal release, memory consolidation, visual performance, sexual drive, modulation of circadian rhythms, and brain development. In the present review, we thoroughly examine the impact of senescence on the dopaminergic system, with a primary focus on the classic delimitations of the dopaminergic nuclei from A8 to A17. We provide in-depth information about their anatomy and function, particularly addressing how senescence affects each of these nuclei.