Miracle-dz/UniFAR-FTUs huggingface dataset:
CDR1 Composition Can Affect Nanobody Recombinant Expression Yields

The isolation of nanobodies from pre-immune libraries by means of biopanning is a straightforward process. Nevertheless, the recovered candidates often require optimization to improve some of their biophysical characteristics. In principle, CDRs are not mutated because they are likely to be part of the antibody paratope, but in this work, we describe a mutagenesis strategy that specifically addresses CDR1. Its sequence was identified as an instability hot spot by the PROSS program, and the available structural information indicated that four CDR1 residues bound directly to the antigen. We therefore modified the loop flexibility with the addition of an extra glycine rather than by mutating single amino acids. This approach significantly increased the nanobody yields but traded-off with moderate affinity loss. Accurate modeling coupled with atomistic molecular dynamics simulations enabled the modifications induced by the glycine insertion and the rationale behind the engineering design to be described in detail.
Corolla Abscission Triggered by Nectar Robbers Positively Affects Reproduction by Enhancing Self-Pollination in Symphytum officinale (Boraginaceae)

Simple Summary Nectar robbers affect plant fitness in different degrees and in different ways, potentially constituting an important part of pollination interactions. While the negative effects of nectar robbing on plant reproductive success have been widely reported, the positive effects are quite unclear. Hence, our study was designed to assess the effects of nectar robbers on reproductive success of Symphytum officinale. This will help in understanding the evolutionary significance of mutualistic relationships between plants and their visitors. Abstract Nectar robbers, which affect plant fitness (directly or indirectly) in different degrees and in different ways, potentially constitute a significant part of mutualistic relationships. While the negative effects of nectar robbing on plant reproductive success have been widely reported, the positive effects remain unknown. The target of our study was to evaluate the effects of nectar robbers on the reproductive success of Symphytum officinale (Boraginaceae). We observed the behavior, species and times of visitors in the field, and we assessed the effect of nectar robbers on corolla abscission rate and time. To test the fitness of corolla abscission, we detected the changes in stigma receptivity, pollen viability, pollen amount and appendage opening size along with the time of flower blossom. The flowering dynamics and floral structure were observed to reveal the mechanism of self-pollination. Finally, pollen deposition seed set rate and fruit set rate were determined to estimate the effect of nectar robbers on reproduction success. We observed 14 species of visitors and 2539 visits in 50 h of observation; 91.7% of them were nectar robbers. The pressure and nectar removal of nectar robbers significantly promoted corolla abscission during a period when pollen grains are viable and the stigma is receptive. In addition, corolla abscission significantly increased the pollen deposition and seed setting rate. Our results demonstrate that nectar robbing contributes to enhancing seed production and positively and indirectly impacts the reproductive success of S. officinale. This mechanism involved the movement of anthers and indirect participation by nectar robbers, which was rarely investigated. Considering the multiple consequences of nectar robbing, understanding the impact of nectar robbers on plant reproduction is essential to comprehend the evolutionary importance of relationships between plants and their visitors.
Connecting Gas-Phase Computational Chemistry to Condensed Phase Kinetic Modeling: The State-of-the-Art

In recent decades, quantum chemical calculations (QCC) have increased in accuracy, not only providing the ranking of chemical reactivities and energy barriers (e.g., for optimal selectivities) but also delivering more reliable equilibrium and (intrinsic/chemical) rate coefficients. This increased reliability of kinetic parameters is relevant to support the predictive character of kinetic modeling studies that are addressing actual concentration changes during chemical processes, taking into account competitive reactions and mixing heterogeneities. In the present contribution, guidelines are formulated on how to bridge the fields of computational chemistry and chemical kinetics. It is explained how condensed phase systems can be described based on conventional gas phase computational chemistry calculations. Case studies are included on polymerization kinetics, considering free and controlled radical polymerization, ionic polymerization, and polymer degradation. It is also illustrated how QCC can be directly linked to material properties.
High Incidence of Related Wolbachia across Unrelated Leaf-Mining Diptera

Simple Summary Polyphagous leaf-mining flies of the genus Liriomyza are pests that pose a serious threat to agricultural and horticultural industries. The endosymbiotic bacterium Wolbachia has been proposed as a useful biocontrol strategy for managing pests, but few studies have so far examined Wolbachia in leafminers. We find a high incidence of related Wolbachia in a survey of infections in 13 dipteran leafminer species collected from Australia and elsewhere which could potentially be useful for the incompatible insect technique (IIT) of pest suppression. We performed curing and crossing experiments on L. brassicae to demonstrate the presence of cytoplasmic incompatibility (CI) needed for IIT, providing a foundation for future transfection of CI Wolbachia from L. brassicae to other Liriomyza pests. Overall, these findings highlight a high incidence of Wolbachia in leaf-mining Diptera, potential horizontal transmission events and possible applications of Wolbachia-based biocontrol strategies for Liriomyza pests. Abstract The maternally inherited endosymbiont, Wolbachia pipientis, plays an important role in the ecology and evolution of many of its hosts by affecting host reproduction and fitness. Here, we investigated 13 dipteran leaf-mining species to characterize Wolbachia infections and the potential for this endosymbiont in biocontrol. Wolbachia infections were present in 12 species, including 10 species where the Wolbachia infection was at or near fixation. A comparison of Wolbachia relatedness based on the wsp/MLST gene set showed that unrelated leaf-mining species often shared similar Wolbachia, suggesting common horizontal transfer. We established a colony of Liriomyza brassicae and found adult Wolbachia density was stable; although Wolbachia density differed between the sexes, with females having a 20-fold higher density than males. Wolbachia density increased during L. brassicae development, with higher densities in pupae than larvae. We removed Wolbachia using tetracycline and performed reciprocal crosses between Wolbachia-infected and uninfected individuals. Cured females crossed with infected males failed to produce offspring, indicating that Wolbachia induced complete cytoplasmic incompatibility in L. brassicae. The results highlight the potential of Wolbachia to suppress Liriomyza pests based on approaches such as the incompatible insect technique, where infected males are released into populations lacking Wolbachia or with a different incompatible infection.
Some microbiological and nutritional properties of Borde and Shamita, traditional Ethiopian fermented beverages

Abstract: Borde and Shamita are two popular fermeated beverages of thick consistency drunk in the southern part of Ethiopia. They are prepared from maize and barely, respectively. The pH values of borde and shamita were 4.1 and 4.2, respectively and counts of aerobic mesophilic bacteria and lactic acid bacteria were high in both products (around 109 cfu/ml). The counts of Enterobacteriaceae was around 106 cfu/ml whereas yeast count ranged between 107 and 108 cfu/ml for both products. In all counts variations within samples were markedly low (coefficient of variation, 5-11 %). Both beverages had comparable protein and fat contents. A third of the borde was soluble. Compared to the raw ingredients, fermentation has resulted in increase in protein, fat and ash contents of the finished products. [Ethiop. J. Health Dev. 1995;9(1):105-110]
Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis

As key inflammatory biomarkers C-reactive protein (CRP) and interleukin-6 (IL6) play an important role in the pathogenesis of non-inflammatory diseases, including specific cancers, such as breast cancer (BC). Previous genome-wide association studies (GWASs) have neither explained the large proportion of genetic heritability nor provided comprehensive understanding of the underlying regulatory mechanisms. We adopted an integrative genomic network approach by incorporating our previous GWAS data for CRP and IL6 with multi-omics datasets, such as whole-blood expression quantitative loci, molecular biologic pathways, and gene regulatory networks to capture the full range of genetic functionalities associated with CRP/IL6 and tissue-specific key drivers (KDs) in gene subnetworks. We applied another systematic genomics approach for BC development to detect shared gene sets in enriched subnetworks across BC and CRP/IL6. We detected the topmost significant common pathways across CRP/IL6 (e.g., immune regulatory; chemokines and their receptors; interferon γ, JAK-STAT, and ERBB4 signaling), several of which overlapped with BC pathways. Further, in gene–gene interaction networks enriched by those topmost pathways, we identified KDs—both well-established (e.g., JAK1/2/3, STAT3) and novel (e.g., CXCR3, CD3D, CD3G, STAT6)—in a tissue-specific manner, for mechanisms shared in regulating CRP/IL6 and BC risk. Our study may provide robust, comprehensive insights into the mechanisms of CRP/IL6 regulation and highlight potential novel genetic targets as preventive and therapeutic strategies for associated disorders, such as BC.
Delignification Effects on Indonesian Momala (Homalium foetidum) and Korean Red Toon (Toona sinensis) Hardwood Pore Structure and Sound Absorption Capabilities

Among the various methods used to improve the sound absorption capability of wood, we focused on delignification in Indonesian momala (Homalium foetidum) and Korean red toon (Toona sinensis). We performed gas permeability, pore size, and porosity analyses and evaluated how the change in the pore structure affects the sound absorption capabilities. Results show that delignification increased the through-pore porosity and improved sound absorption capability in both species. In addition, the air gap in the rear space maximized the sound absorption of momala and the red toon. The noise reduction coefficient (NRC) of delignified momala (90 min) with a 3 cm air gap was 0.359 ± 0.023. This is approximately 154.6% higher than that of untreated momala without an air gap. The NRC of delignificated red toon (90 min) with a 3 cm air gap was 0.324 ± 0.040, an increase of 604.3% over untreated red toon without an air gap.
In Vivo Distribution of Poly(ethylene glycol) Functionalized Iron Oxide Nanoclusters: An Ultrastructural Study

The in vivo distribution of 50 nm clusters of polyethylene glycol-conjugated superparamagnetic iron oxide nanoparticles (SPIONs-PEG) was conducted in this study. SPIONs-PEG were synthesized de novo, and their structure and paramagnetic behaviors were analyzed by specific methods (TEM, DLS, XRD, VSM). Wistar rats were treated with 10 mg Fe/kg body weight SPIONs-PEG and their organs and blood were examined at two intervals for short-term (15, 30, 60, 180 min) and long-term (6, 12, 24 h) exposure evaluation. Most exposed organs were investigated through light and transmission electron microscopy, and blood and urine samples were examined through fluorescence spectrophotometry. SPIONs-PEG clusters entered the bloodstream after intraperitoneal and intravenous administrations and ended up in the urine, with the highest clearance at 12 h. The skin and spleen were within normal histological parameters, while the liver, kidney, brain, and lungs showed signs of transient local anoxia or other transient pathological affections. This study shows that once internalized, the synthesized SPIONs-PEG disperse well through the bloodstream with minor to nil induced tissue damage, are biocompatible, have good clearance, and are suited for biomedical applications.
Identifying Clinicopathological Factors Associated with Oncotype DX® 21-Gene Recurrence Score: A Real-World Retrospective Cohort Study of Breast Cancer Patients in Quebec City, Canada

Gene expression profiling tests such as the Oncotype DX (ODX) 21-gene recurrence score (RS) assay is increasingly used in clinical practice to predict the risk of recurrence and support treatment planning for early-stage breast cancer (BC). However, this test has some disadvantages such as a high cost and a long turnaround time to get results, which may lead to disparities in access. We aim to identify clinicopathological factors associated with ODX RS in women with early-stage BC. We conducted a retrospective cohort study of women identified in the medical database of the Deschênes-Fabia Breast Disease Center of Quebec City University, Canada. Our sample consists of 425 women diagnosed with early-stage BC who have obtained an ODX RS between January 2011 and April 2015. The ODX RS has been categorized into three levels as originally defined: low (0–17), intermediate (18–30), and high (>30). The mean RS was 17.8 (SD = 9.2). Univariate analyses and multinomial logistic regressions were performed to identify factors associated with intermediate and high RS compared with low RS. A total of 237 (55.8%) patients had low RS, 148 (34.8%) had intermediate RS, and 40 (9.4%) had high RS. Women with progesterone receptor (PR)-negative (ORs ranging from 3.51 to 10.34) and histologic grade II (ORs ranging from 3.16 to 23.04) tumors were consistently more likely to have intermediate or high RS than low RS. Similar patterns of associations were observed when the RS was categorised using redefined thresholds from (i.e., from the TAILORx study or dichotomized). This study provides evidence suggesting that histologic grade and PR status are predictive factors for intermediate or high RS in women with early-stage BC. If these results are confirmed in future studies, considering these clinicopathological factors could spare women the need to get such a test before the beginning of a possible adjuvant therapy. This option could be considered in settings where the cost of testing is an issue.
Occurrence of Intestinal Parasites of Public Health Significance in Fresh Horticultural Products Sold in Maputo Markets and Supermarkets, Mozambique

(1) Background: Giardia duodenalis and Cryptosporidium are important neglected parasites associated with diarrhea, such as the emerging Enterocytozoon bieneusi. All three are foodborne parasites raising concerns in public health. This study intended to understand the intestinal parasite occurrence with emphasis on G. duodenalis, Cryptosporidium, and E. bieneusi in fresh fruits/vegetables sold in the main municipal markets of Maputo city, Mozambique. (2) Methods: A total of 321 fresh horticultural products were purchased in the rainy and dry seasons (five markets/two supermarkets/one agricultural zone). Light microscopy (LM) and PCR analysis were performed. (3) Results: By LM and/or PCR, 29.3% of the samples presented at least one parasite (rainy season: 22.9%; dry season: 35.1%). The most contaminated horticultural products: collected in dry season, from Zimpeto and Fajardo markets, lettuce and pointed white cabbage. Overall, 3.7% of G. duodenalis, 1.3% of E. bieneusi, and other intestinal parasites (pathogenic and non-pathogenic) were identified. (4) Conclusions: Important pathogenic intestinal parasites were identified in fruits/vegetables commercially purchased in Maputo City. This fact must be taken into consideration when planning the management of these horticultural markets, in order to reduce the risk of contamination of fresh produce by intestinal parasites, and to prevent foodborne diseases.
Synthesis and Characterization of PdAgNi/C Trimetallic Nanoparticles for Ethanol Electrooxidation

The direct use of ethanol in fuel cells presents unprecedented economic, technical, and environmental opportunities in energy conversion. However, complex challenges need to be resolved. For instance, ethanol oxidation reaction (EOR) requires breaking the rigid C–C bond and results in the generation of poisoning carbonaceous species. Therefore, new designs of the catalyst electrode are necessary. In this work, two trimetallic PdxAgyNiz/C samples are prepared using a facile borohydride reduction route. The catalysts are characterized by X-ray diffraction (XRD), Energy-Dispersive X-ray spectroscopy (EDX), X-ray photoelectron Spectroscopy (XPS), and Transmission Electron Microscopy (TEM) and evaluated for EOR through cyclic voltammetry (CV), chronoamperometry (CA), and electrochemical impedance spectroscopy (EIS). The XRD patterns have shown a weak alloying potential between Pd, and Ag prepared through co-reduction technique. The catalysts prepared have generally shown enhanced performance compared to previously reported ones, suggesting that the applied synthesis may be suitable for catalyst mass production. Moreover, the addition of Ag and Ni has improved the Pd physiochemical properties and electrocatalytic performance towards EOR in addition to reducing cell fabrication costs. In addition to containing less Pd, The PdAgNi/C is the higher performing of the two trimetallic samples presenting a 2.7 A/mgPd oxidation current peak. The Pd4Ag2Ni1/C is higher performing in terms of its steady-state current density and electrochemical active surface area.
Glimepiride-Loaded Nanoemulgel; Development, In Vitro Characterization, Ex Vivo Permeation and In Vivo Antidiabetic Evaluation

Glimepiride (GMP), an oral hypoglycemic agent is extensively employed in the treatment of type 2 diabetes. Transdermal delivery of GMP has been widely investigated as a promising alternative to an oral approach but the delivery of GMP is hindered owing to its low solubility and permeation. The present study was designed to formulate topical nanoemulgel GMP system and previously reported solubility enhanced glimepiride (GMP/βCD/GEL-44/16) in combination with anti-diabetic oil to enhance the hypoglycemic effect. Nanoemulsions were developed using clove oil, Tween-80, and PEG-400 and were gelled using xanthan gum (3%, w/w) to achieve the final nanoemulgel formulations. All of the formulations were evaluated in terms of particle size, zeta potential, pH, conductivity, viscosity, and in vitro skin permeation studies. In vivo hypoglycemic activity of the optimized nanoemulgel formulations was evaluated using a streptozocin-induced diabetes model. It was found that a synergistic combination of GMP with clove oil improved the overall drug permeation across the skin membrane and the hypoglycemic activity of GMP. The results showed that GMP/βCD/GEL-44/16-loaded nanoemulgel enhanced the in vitro skin permeation and improved the hypoglycemic activity in comparison with pure and marketed GMP. It is suggested that topical nano emulsion-based GMP gel and GMP/βCD/GEL-44/16 could be an effective alternative for oral therapy in the treatment of diabetes.
Overexpression of 7-hydroxymethyl Chlorophyll a Reductase from Cucumber in Tobacco Accelerates Dark-Induced Chlorophyll Degradation

7-hydroxymethyl chlorophyll (Chl) a reductase (HCAR) plays critical roles in the Chl cycle and degradation during leaf senescence, however, its function in horticultural crops remains unknown. Here, we identified an HCAR gene (CsHCAR) from cucumber (Cucumis sativus L.) and investigated its roles in response to dark-induced Chl degradation. CsHCAR encoded 459 amino acids, which were orthologous to Arabidopsis HCAR, had the conserved domains, and localized in the chloroplast. Gene expression analysis showed that CsHCAR expression was the highest in senescent leaves and was responsive to different stresses and phytohormone treatments. Overexpression of CsHCAR in tobacco accelerated dark-induced Chl degradation through enhancing the expression of Chl catabolic genes. After 10 d of darkness treatment, the biomass of CsHCAR overexpression plants was reduced. Furthermore, the value of net photosynthetic rate, maximum quantum yield of photosystem II, and effective quantum yield of photosystem II in CsHCAR overexpression plants was significantly reduced in comparison to that in wild-type (WT) plants. The photosynthetic protein content, including Lhcb1, Lhcb2, Lhcb4, RbcS, and RbcL in CsHCAR overexpression plants exhibited a lower level as compared to that observed in WT plants. In addition, the expression of genes encoding these proteins in CsHCAR overexpression plants was significantly lower than that in WT plants. Moreover, CsHCAR overexpression plants inhibited the dark-induced accumulation of reactive oxygen species (ROS). These results indicate that CsHCAR affects the stability of photosynthetic proteins in chloroplasts, positively regulates Chl degradation, and plays an important role in maintaining ROS homeostasis in leaves.
Parasites Circulating in Wild Synanthropic Capybaras (Hydrochoerus hydrochaeris): A One Health Approach

Capybaras (Hydrochoerus hydrochaeris) are affected by a wide range of protozoan and metazoan-derived parasitic diseases. Among parasites of free-ranging capybaras are soil-, water-, food- and gastropod-borne parasitosis, today considered as opportunistic infections in semiaquatic ecosystems. The overlapping of the capybara’s natural ecological habitats with human and domestic animal activities has unfortunately increased in recent decades, thereby enhancing possible cross- or spillover events of zoonotic parasites. Due to this, three synanthropic wild capybara populations in the Orinoco Basin were studied for the occurrence of gastrointestinal parasite infections. A total of forty-six fecal samples were collected from free-ranging capybaras in close proximity to livestock farms. Macroscopical analyses, standard copromicroscopical techniques, coproELISA, PCR, and phylogenetic analysis revealed thirteen parasite taxa. In detail, the study indicates stages of five protozoans, four nematodes, one cestode, and three trematodes. Two zoonotic parasites were identified (i.e., Plagorchis muris, and Neobalantidium coli). The trematode P. muris represents the first report within South America. In addition, this report expands the geographical distribution range of echinocoelosis (Echinocoleus hydrochoeri). Overall, parasitological findings include two new host records (i.e., P. muris, and Entamoeba). The present findings collectively constitute baseline data for future monitoring of wildlife-derived anthropozoonotic parasites and call for future research on the health and the ecological impact of this largest semiaquatic rodent closely linked to humans, domestic and wild animals.
Beta vulgaris as a Natural Nitrate Source for Meat Products: A Review

Curing meat products is an ancient strategy to preserve muscle foods for long periods. Nowadays, cured meat products are widely produced using nitrate and nitrite salts. However, the growing of the clean-label movement has been pushing to replace synthetic nitrate/nitrite salts (indicated as E-numbers in food labels) with natural ingredients in the formulation of processed foods. Although no ideal synthetic nitrate/nitrite replacements have yet been found, it is known that certain vegetables contain relevant amounts of nitrate. Beta vulgaris varieties (Swiss chard/chard, beetroot, and spinach beet, for instance) are widely produced for human consumption and have relevant amounts of nitrate that could be explored as a natural ingredient in cured meat product processing. Thus, this paper provides an overview of the main nitrate sources among Beta vulgaris varieties and the strategic use of their liquid and powder extracts in the production of cured meat products.