Probing Protein-Ligand Methyl-π Interaction Geometries through Chemical Shift Measurements of Selectively Labeled Methyl Groups.

Fragment-based drug design is heavily dependent on the optimization of initial low-affinity binders. Herein we introduce an approach that uses selective labeling of methyl groups in leucine and isoleucine side chains to directly probe methyl-π contacts, one of the most prominent forms of interaction between proteins and small molecules. Using simple NMR chemical shift perturbation experiments with selected BRD4-BD1 binders, we find good agreement with a commonly used model of the ring-current effect as well as the overall interaction geometries extracted from the Protein Data Bank. By combining both interaction geometries and chemical shift calculations as fit quality criteria, we can position dummy aromatic rings into an AlphaFold model of the protein of interest. The proposed method can therefore provide medicinal chemists with important information about binding geometries of small molecules in fast and iterative matter, even in the absence of high-resolution experimental structures.

Combined Effect of Nigella sativa and Kefir on the Live Performance and Health of Broiler Chickens Affected by Necrotic Enteritis.

Coccidiosis and necrotic enteritis (NE) are prevalent poultry ailments worldwide, leading to decreased live performance and elevated mortality rates without antibiotic usage. This study evaluated Nigella sativa (black cumin) seeds (BCS) and kefir as alternatives to antibiotics for broilers. An in vivo study over a 28-day period, using 384 Cobb 500 male broilers organized into six treatment groups as part of a completely randomized block experimental design was conducted. Each treatment group included eight replicates, with each replicate containing eight birds. The treatments included positive control, negative control, antibiotic control, 5% BCS in feed, 20% kefir in drinking water, and a combination of 5% BCS and 20% kefir. NE was induced in broilers by administering ~5000 oocysts of Eimeria maxima orally on day 14, followed by inoculation with about 108 CFU/mL of Clostridium perfringens (Cp) (strain Cp#4) on days 19, 20, and 21. Live performance metrics including feed intake, body weight gain, and feed conversion were assessed in broilers. Additionally, NE disease outcomes such as lesion scores, mortality rates, and Cp populations in cecum were determined during the study. The BCS, kefir, and the combination had no detrimental effect on broiler live performance. BCS-treated and combination groups had lower NE scores (p > 0.05) in comparison to the positive control and exhibited no significant difference (p > 0.05) from antibiotic control. Additionally, treatment groups and antibiotic control were not significantly different (p > 0.05) in mortality, whereas the BCS and kefir combination significantly reduced (p < 0.05) mortality to 14.1% compared to 31.3% for the positive control. C. perfringens vegetative cells significantly decreased (p < 0.05) in treatments with BCS, kefir, and their combination on days 22 and 28 compared to the positive control. On day 22, Cp sores were significantly lower (p < 0.05) for the kefir and combination treatments compared to the positive control. In conclusion, BCS and kefir successfully reduced C. perfringens infection and mortality without any detrimental impact on broiler live performance with the combined treatment being the most effective. These results suggest that BCS and kefir could serve as potential alternatives to antibiotics in managing NE.

Frequency of use and annual costs of biological therapy for psoriasis in Colombia in 2019.

BACKGROUND: Evidence describing the types and annual costs of biological treatments for psoriasis in Latin America is scarce. This study aimed to estimate the frequency of use and costs of biologic therapy for psoriasis in Colombia in 2019. METHODS: This secondary data analysis uses the International Classification of Diseases terms associated with psoriasis, excluding those related to psoriatic arthritis, based on data from the registry of the Colombian Ministry of Health. We estimated the prevalence of psoriasis per 100,000 inhabitants; then, we retrieved the frequency of use of biologic therapy in patients with psoriasis and estimated the cost per year of each and overall therapies in 2019 in US dollars (USD). RESULTS: There were 100,823 patients with psoriasis in Colombia in 2019, which amounts to a prevalence of 0.2% in the general population. Of those patients, 4.9% received biologic therapy, most frequently males (60%). The most commonly used biological therapies for psoriasis in Colombia in 2019 were ustekinumab (35.2%), with an annual cost per patient of $12,880 USD; adalimumab (26%), with a yearly cost per patient of $7130 USD; and secukinumab (19.8%), with an annual cost per patient of $6825 USD. CONCLUSION: This is the first study to describe the use and cost of biological therapy for psoriasis in Colombia. It provides valuable cost-awareness information for the Colombian health system.

[Lamellar macular holes-In the center of vitreomacular interface diseases : Pathophysiology, spontaneous courses and treatment concepts]. / Makulaschichtforamen ­ im Zentrum der vitreomakulären Grenzflächenerkrankungen : Pathophysiologie, Spontanverläufe und Therapiekonzepte.

BACKGROUND: A lamellar macular hole (LMH) is characterized by a distinct morphologic configuration and can be distinguished from related entities such as macular pseudohole (MPH) and epiretinal membrane with foveoschisis (ERM-FS) by clear morphologic features. PURPOSE: Based on current knowledge, the pathophysiologic function of LMH in the spectrum of vitreomacular interface diseases will be described and therapeutic concepts will be presented. METHODS: Current studies are supplemented by case reports to provide a schematic overview of the natural history and therapeutic concepts at the vitreomacular interface. RESULTS: The LMH is as a retrospective marker for pathologic posterior vitreous detachment in adult patients and may be interpreted as the pathophysiologic center of tractional maculopathies. Various vitreomacular pathologies can result in LMH: a detached vitreomacular traction, a spontaneously closed penetrating macular hole, or an epiretinal membrane with foveoschisis. Pathophysiologically, a degenerative, progressive loss of the architecture of the foveal muller cell cone may be the underlaying mechanism, resulting in the typical undermining of the hole edges and occasionally in a full thickness macular hole. The optimal timing and the appropriate surgical method are the focus of current clinical studies. CONCLUSION: The pathophysiology of LMH indicates a smooth transition of tractive maculopathies. These should be prospectively evaluated in order to develop evidence-based treatment strategies for LMH.

Carbapenem-resistant Acinetobacter baumannii complex in the United States-An epidemiological and molecular description of isolates collected through the Emerging Infections Program, 2019.

BACKGROUND: Understanding the epidemiology of carbapenem-resistant A. baumannii complex (CRAB) and the patients impacted is an important step toward informing better infection prevention and control practices and improving public health response. METHODS: Active, population-based surveillance was conducted for CRAB in 9 U.S. sites from January 1 to December 31, 2019. Medical records were reviewed, isolates were collected and characterized including antimicrobial susceptibility testing and whole genome sequencing. RESULTS: Among 136 incident cases in 2019, 66 isolates were collected and characterized; 56.5% were from cases who were male, 54.5% were from persons of Black or African American race with non-Hispanic ethnicity, and the median age was 63.5 years. Most isolates, 77.2%, were isolated from urine, and 50.0% were collected in the outpatient setting; 72.7% of isolates harbored an acquired carbapenemase gene (aCP), predominantly blaOXA-23 or blaOXA-24/40; however, an isolate with blaNDM was identified. The antimicrobial agent with the most in vitro activity was cefiderocol (96.9% of isolates were susceptible). CONCLUSIONS: Our surveillance found that CRAB isolates in the U.S. commonly harbor an aCP, have an antimicrobial susceptibility profile that is defined as difficult-to-treat resistance, and epidemiologically are similar regardless of the presence of an aCP.

Assessing pollution degree and human health risks from hazardous element distribution in soils near gold mines in a Colombian Andean region: Correlation with phytotoxicity biomarkers.

The assessment of human health risk due to the presence of hazardous elements in the environment is now necessary for environmental management and legislative initiatives. This study aims to determine the contamination by As, Cd, Pb, and Cr in soils near gold mines in three municipalities located in the Andean region of Colombia. One of the main objectives of the study is to explore possible correlations between the Lifetime Cancer Risk (LCR) and phytotoxicity biomarkers using a simple and rapid-response plant model, radish (Raphanus sativus L.). In the municipality of Yalí, Puerto Berrío, and Buriticá, the hazardous elements concentrations ranged from 8.1 to 35.5, 1.7 to 892, and 5.8 to 49.8 for As, 0.1 to 4.6, 0.1 to 65.2, and 0.5 to 18.2 for Cd, 18.5 to 201.3, 13.0 to 1908, and 189 to 2345 for Pb, and 5.4 to 118.4, 65.4 to 301, and 5.4 to 102.3 for Cr, respectively. The results showed that the biomarkers intracellular H2O2 concentration, antioxidant activity, and radicle elongation exhibited significant (P < 0.05) variations associated with the concentration of hazardous elements in the soils. Significant correlations (P < 0.05, r > 0.58) were found between the biomarkers and the LCR for Cd, Pb, and Cr, but not for As. The results using biomarkers reveal that soil pH and organic matter content are important variables that control the bioavailability of these elements in the soil. The use of indicators like LCR alone has limitations and should be accompanied by the use of biomarkers that allow for a better understanding of the biological system's response to exposure to potentially toxic elements. The results obtained show the urgent need to implement public policies to minimize exposure to hazardous substances in areas near gold mining projects.

Glyphosate modifies the gene expression and migration of trophoblastic cells without altering the process of angiogenesis or the implantation of blastocysts in vitro.

Adverse pregnancy outcomes have been associated with the presence of glyphosate (G) in umbilical cord, serum, and urine samples from pregnant women. Our aim was to study the effect of G on blastocyst implantation using an in vitro mouse model, and the migration and acquisition of endothelial phenotype of the human trophoblastic HTR8/SVneo (H8) cells. In mouse blastocysts, no differences in attachment time and implantation outgrowth area were observed after G exposure. H8 cell migration was stimulated by 0.625 µM G without cytotoxicity. After 6 h, the mRNA expression of vascular endothelial growth factor (VEGF) and C-C motif chemokine ligand 2 (CCL2) was upregulated in H8 cells exposed to 1.25 µM G when compared vehicle-treated cells (p ≤ 0.05). No differences were observed in interleukin 11, VEGF receptor 1, and coagulation factor II thrombin receptor in H8 cells exposed to different concentrations of G for 6 h compared to the vehicle. Interestingly, exposure to G did not alter angiogenesis as measured by a tube formation assay. Taken all together, these results suggest that G exposure may contribute as a risk factor during pregnancy, due to its ability to alter trophoblast migration and gene expression.

Combining anaerobic digestion slurry and different biochars to develop a biochar-based slow-release NPK fertilizer.

In this research, we developed a biochar-based fertilizer using biogas slurry and biochar derived from lignocellulosic agro-residues. Biogas slurry was obtained through the anaerobic digestion of the organic fraction of municipal solid waste (fresh vegetable biomass and/or prepared food), while biochars were derived from residues from quinoa, maize, rice, and sugarcane. The biochar-based fertilizers were prepared using an impregnation process, where the biogas slurry was mixed with each of the raw biochars. Subsequently, we characterized the N, P and K concentrations of the obtained biochar-based fertilizers. Additionally, we analyzed their surface properties using SEM/EDS and FTIR and conducted a slow-release test on these biochar-based fertilizers to assess their capability to gradually release nutrients. Lastly, a bioassay using cucumber plants was conducted to determine the N, P, and K bioavailability. Our findings revealed a significant correlation (r > 0.67) between the atomic O/C ratio, H/C ratio, cation exchange capacity, surface area, and the base cations concentration with N, P, and/or K adsorption on biochar. These properties, in turn, were linked to the capability of the biochar-based fertilizer to release nutrients in a controlled manner. The biochar-based fertilizer derived from corn residues showed <15 % release of N, P and K at 24 h. Utilization of these biochar-based fertilizers had a positive impact on the mineral nutrition of cucumber plants, resulting in an average increase of 61 % in N, 32 % in P, and 19 % in K concentrations. Our results underscore the potential of biochar-based fertilizers in controlled nutrient release and enhanced plant nutrition. Integration of biochar and biogas slurry offers a promising and sustainable approach for NPK recovery and fertilizer production in agriculture. This study presents an innovative and sustainable approach combining the use of biochar for NPK recovery from biogas slurry and its use as a biochar-based fertilizer in agriculture.

Correction: Inferring school district learning modalities during the COVID-19 pandemic with a hidden Markov model.

[This corrects the article DOI: 10.1371/journal.pone.0292354.].

Mutagenesis techniques for evolutionary engineering of microbes - exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases.

The natural process of evolutionary adaptation is often exploited as a powerful tool to obtain microbes with desirable traits. For industrial microbes, evolutionary engineering is often used to generate variants that show increased yields or resistance to stressful industrial environments, thus obtaining superior microbial cell factories. However, even in large populations, the natural supply of beneficial mutations is typically low, which implies that obtaining improved microbes is often time-consuming and inefficient. To overcome this limitation, different techniques have been developed that boost mutation rates. While some of these methods simply increase the overall mutation rate across a genome, others use recent developments in DNA synthesis, synthetic biology, and CRISPR-Cas techniques to control the type and location of mutations. This review summarizes the most important recent developments and methods in the field of evolutionary engineering in model microorganisms. It discusses how both in vitro and in vivo approaches can increase the genetic diversity of the host, with a special emphasis on in vivo techniques for the optimization of metabolic pathways for precision fermentation.

Bringing into focus the central domains C3-C6 of myosin binding protein C.

Myosin binding protein C (MyBPC) is a multi-domain protein with each region having a distinct functional role in muscle contraction. The central domains of MyBPC have often been overlooked due to their unclear roles. However, recent research shows promise in understanding their potential structural and regulatory functions. Understanding the central region of MyBPC is important because it may have specialized function that can be used as drug targets or for disease-specific therapies. In this review, we provide a brief overview of the evolution of our understanding of the central domains of MyBPC in regard to its domain structures, arrangement and dynamics, interaction partners, hypothesized functions, disease-causing mutations, and post-translational modifications. We highlight key research studies that have helped advance our understanding of the central region. Lastly, we discuss gaps in our current understanding and potential avenues to further research and discovery.

Ligandability assessment of the C-terminal Rel-homology domain of NFAT1.

Transcription factors are generally considered challenging, if not "undruggable", targets but they promise new therapeutic options due to their fundamental involvement in many diseases. In this study, we aim to assess the ligandability of the C-terminal Rel-homology domain of nuclear factor of activated T cells 1 (NFAT1), a TF implicated in T-cell regulation. Using a combination of experimental and computational approaches, we demonstrate that small molecule fragments can indeed bind to this protein domain. The newly identified binder is the first small molecule binder to NFAT1 validated with biophysical methods and an elucidated binding mode by X-ray crystallography. The reported eutomer/distomer pair provides a strong basis for potential exploration of higher potency binders on the path toward degrader or glue modalities.

Hypertrophic cardiomyopathy in MYBPC3 carriers in aging.

Hypertrophic cardiomyopathy (HCM) is characterized by abnormal thickening of the myocardium, leading to arrhythmias, heart failure, and elevated risk of sudden cardiac death, particularly among the young. This inherited disease is predominantly caused by mutations in sarcomeric genes, among which those in the cardiac myosin binding protein-C3 (MYBPC3) gene are major contributors. HCM associated with MYBPC3 mutations usually presents in the elderly and ranges from asymptomatic to symptomatic forms, affecting numerous cardiac functions and presenting significant health risks with a spectrum of clinical manifestations. Regulation of MYBPC3 expression involves various transcriptional and translational mechanisms, yet the destiny of mutant MYBPC3 mRNA and protein in late-onset HCM remains unclear. Pathogenesis related to MYBPC3 mutations includes nonsense-mediated decay, alternative splicing, and ubiquitin-proteasome system events, leading to allelic imbalance and haploinsufficiency. Aging further exacerbates the severity of HCM in carriers of MYBPC3 mutations. Advancements in high-throughput omics techniques have identified crucial molecular events and regulatory disruptions in cardiomyocytes expressing MYBPC3 variants. This review assesses the pathogenic mechanisms that promote late-onset HCM through the lens of transcriptional, post-transcriptional, and post-translational modulation of MYBPC3, underscoring its significance in HCM across carriers. The review also evaluates the influence of aging on these processes and MYBPC3 levels during HCM pathogenesis in the elderly. While pinpointing targets for novel medical interventions to conserve cardiac function remains challenging, the emergence of personalized omics offers promising avenues for future HCM treatments, particularly for late-onset cases.

High-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia.

Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adapter protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, BCH-HSP-C01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate potential mechanisms of action of BCH-HSP-C01. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future studies.

Phosphorus-Loaded Biochar-Assisted Phytoremediation to Immobilize Cadmium, Chromium, and Lead in Soils.

Soil contamination with heavy metals (HM) poses significant challenges to food security and public health, requiring the exploration of effective remediation strategies. This study aims to evaluate the remediation process of soils contaminated with Cd, Cr, and Pb using Lolium perenne assisted by four types of biochar: (i) activated coffee husk biochar (BAC), (ii) nonactivated biochar coffee husk (BSAC), (iii) activated sugar cane leaf biochar (BAA), and (iv) nonactivated biochar sugar cane leaf (BSAA). Biochar, loaded with phosphorus (P), was applied to soils contaminated with Cd, Cr, and Pb. L. perenne seedlings, averaging 2 cm in height, were planted. The bioavailability of P and heavy metals (HM) was monitored every 15 days until day 45, when the seedlings reached an average height of 25 cm. At day 45, plant harvesting was conducted and stems and roots were separated to determine metal concentrations in both plant parts and the soil. The study shows that the combined application of biochar and L. perenne positively influences the physicochemical properties of the soil, resulting in an elevation of pH and electrical conductivity (EC). The utilization of biochar contributes to an 11.6% enhancement in the retention of HM in plant organs. The achieved bioavailability of heavy metals in the soil was maintained at levels of less than 1 mg/kg. Notably, Pb exhibited a higher metal retention in plants, whereas Cd concentrations were comparatively lower. These findings indicate an increase in metal immobilization efficiencies when phytoremediation is assisted with P-loaded biochar. This comprehensive assessment highlights the potential of biochar-assisted phytoremediation as a promising approach for mitigating heavy metal contamination in soils.