Miracle-dz/UniFAR-FTUs huggingface dataset:
Hyperosmotic stress in Chlamydomonas induces metabolomic changes in biosynthesis of complex lipids

ABSTRACT To study the early stress response of the green microalga Chlamydomonas reinhardtii CC-503, we exposed cells to hyperosmotic conditions for a period of 5 hours, sampling at eight time points. We performed metabolomic analysis of primary metabolism using gas chromatography/time-of-flight mass spectrometry (GC-TOF MS), and lipidomic analysis by liquid chromatography/quadrupole time-of-flight mass spectrometry (CSH-QTOF MS). Under hyperosmotic stress, many mono- and disaccharides increased along with the concentrations of sugar alcohols similar to osmoprotectants in higher plants. The levels of 13 proteinogenic amino acids increased, suggesting increased biosynthesis over the course of 5 hours, which is clearly a slower response than carbohydrate metabolism. TCA cycle compounds decreased in a tightly co-regulated manner under hyperosmotic stress as a cataplerotic reaction to provide carbon backbones for amino acid biosynthesis. Of note, levels of free palmitoyl-compounds (palmitic acid and monopalmitin) decreased over the stress time course in an opposite pattern to the increase in stearoyl compounds. Triglycerides that increased in concentration under osmotic stress were on average three carbons longer and had four more double bonds compared with triglycerides that remained unchanged. Along with the difference in C18-fatty acids compared with C16-fatty acids, these changes may indicate a specific activation of elongases and desaturases or remodelling from membrane acyl-lipids towards triacylglcyerides.
Comprehensive Analysis of Human microRNA–mRNA Interactome

MicroRNAs play a key role in the regulation of gene expression. A majority of microRNA-mRNA interactions remain unidentified. Despite extensive research, our ability to predict human microRNA-mRNA interactions using computational algorithms remains limited by a complexity of the models for non-canonical interactions, and an abundance of false positive results. Here we present the landscape of microRNA-mRNA human interactions, which we derived from comprehensive analysis of datasets describing direct microRNA-mRNA interactions experimentally defined in HEK293 and Huh7.5 cell lines, along with other available microRNA and mRNA expression data. We have also established a collection of reliable microRNA binding regions that we systematically extracted in course of analysis of 79 CLIP datasets, which is available at http://score.generesearch. ru/services/mirna/. While only 1-2% of human genes interact with microRNAs, some RNAs display a substantial sponge effect, which is specific to the cell line of study. Some microRNAs are expressed at a very high level, while interacting with only a few mRNAs, thus, indeed, serving as specific gene expression regulators. Other miRNAs might be expressed at relatively low levels, and interact with many mRNAs. Some of the microRNAs might switch between these two classes, depending on cellular context. Results of our study provide an initial resolution into the complex patterns of human microRNA-mRNA interactions.
Noninvasive Phenotyping of Plant–Pathogen Interaction: Consecutive In Situ Imaging of Fluorescing Pseudomonas syringae, Plant Phenolic Fluorescence, and Chlorophyll Fluorescence in Arabidopsis Leaves

Plant–pathogen interactions have been widely studied, but mostly from the site of the plant secondary defense. Less is known about the effects of pathogen infection on plant primary metabolism. The possibility to transform a fluorescing protein into prokaryotes is a promising phenotyping tool to follow a bacterial infection in plants in a noninvasive manner. In the present study, virulent and avirulent Pseudomonas syringae strains were transformed with green fluorescent protein (GFP) to follow the spread of bacteria in vivo by imaging Pulse-Amplitude-Modulation (PAM) fluorescence and conventional binocular microscopy. The combination of various wavelengths and filters allowed simultaneous detection of GFP-transformed bacteria, PAM chlorophyll fluorescence, and phenolic fluorescence from pathogen-infected plant leaves. The results show that fluorescence imaging allows spatiotemporal monitoring of pathogen spread as well as phenolic and chlorophyll fluorescence in situ, thus providing a novel means to study complex plant–pathogen interactions and relate the responses of primary and secondary metabolism to pathogen spread and multiplication. The study establishes a deeper understanding of imaging data and their implementation into disease screening.
Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants

Abstract Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.
IHC Color Histograms for Unsupervised Ki67 Proliferation Index Calculation

Automated image analysis tools for Ki67 breast cancer digital pathology images would have significant value if integrated into diagnostic pathology workflows. Such tools would reduce the workload of pathologists, while improving efficiency, and accuracy. Developing tools that are robust and reliable to multicentre data is challenging, however, differences in staining protocols, digitization equipment, staining compounds, and slide preparation can create variabilities in image quality and color across digital pathology datasets. In this work, a novel unsupervised color separation framework based on the IHC color histogram (IHCCH) is proposed for the robust analysis of Ki67 and hematoxylin stained images in multicentre datasets. An “overstaining” threshold is implemented to adjust for background overstaining, and an automated nuclei radius estimator is designed to improve nuclei detection. Proliferation index and F1 scores were compared between the proposed method and manually labeled ground truth data for 30 TMA cores that have ground truths for Ki67+ and Ki67− nuclei. The method accurately quantified the PI over the dataset, with an average proliferation index difference of 3.25%. To ensure the method generalizes to new, diverse datasets, 50 Ki67 TMAs from the Protein Atlas were used to test the validated approach. As the ground truth for this dataset is PI ranges, the automated result was compared to the PI range. The proposed method correctly classified 74 out of 80 TMA images, resulting in a 92.5% accuracy. In addition to these validations experiments, performance was compared to two color-deconvolution based methods, and to six machine learning classifiers. In all cases, the proposed work maintained more consistent (reproducible) results, and higher PI quantification accuracy.
Cytotoxic and gene expression study of KRAS gene in lung cancer cell line of A549 treated with Tinospora cordifolia extract

Normally, normal cells multiply to form new cells and worn out cells are removed in an orderly manner. This is regulated by process controlled by many enzymes and checkpoints. Cancer is initiated when this controlled process is deregulated and cells in any particular part of the body start multiplying in an uncontrolled fashion. These cancerous cells are different from normal cells in many ways which include their growth pattern and cell death mechanism. [1] Cancerous cells do not die as they deregulate the normal cell death mechanisms and continuously multiply. These altered cells also gain the ability to invade other tissues and parts of the body to form secondary tumors.
Prospects for the use of “protected fats” in cattle feed additives

The article reviews the use and physiological effects of fats protected from decay in the rumen of ruminants, as well as types of feed additives containing “protected fats”, presents their comparative characteristics of fatty acid composition, indicators of exchange and pure lactation energy. Summarized data indicate the prospects of the technology of “protected fats” and their use in animal husbandry.
Novel Model for Comprehensive Assessment of Robust Prognostic Gene Signature in Ovarian Cancer Across Different Independent Datasets

Different analytical methods or models can often find completely different prognostic biomarkers for the same cancer. In the study of prognostic molecular biomarkers of ovarian cancer (OvCa), different studies have reported a variety of prognostic gene signatures. In the current study, based on geometric concepts, the linearity-clustering phase diagram with integrated P-value (LCP) method was used to comprehensively consider three indicators that are commonly employed to estimate the quality of a prognostic gene signature model. The three indicators, namely, concordance index, area under the curve, and level of the hazard ratio were determined via calculation of the prognostic index of various gene signatures from different datasets. As evaluation objects, we selected 13 gene signature models (Cox regression model) and 16 OvCa genomic datasets (including gene expression information and follow-up data) from published studies. The results of LCP showed that three models were universal and better than other models. In addition, combining the three models into one model showed the best performance in all datasets by LCP calculation. The combination gene signature model provides a more reliable model and could be validated in various datasets of OvCa. Thus, our method and findings can provide more accurate prognostic biomarkers and effective reference for the precise clinical treatment of OvCa.
CD28 Deficiency Ameliorates Blast Exposure-Induced Lung Inflammation, Oxidative Stress, Apoptosis, and T Cell Accumulation in the Lungs via the PI3K/Akt/FoxO1 Signaling Pathway

Although CD28 is associated with the expression of inflammatory mediators, apoptosis-related protein, immunosuppression, and tumorigenesis, the effects of CD28 deficiency on blast exposure-induced lung injury have not been investigated. In this study, we have explored the effects of CD28 on blast exposure-induced lung injury and studied its potential molecular mechanisms. A mouse model of blast exposure-induced acute lung injury was established. Sixty C57BL/6 wild-type (WT) and CD28 knockout (CD28−/−) mice were randomly divided into control or model groups. Lung tissue samples were collected 24 h and 48 h after blast injury. Histopathological changes and the expressions of inflammatory-related proteins were detected by hematoxylin-eosin, immunohistochemistry, and immunofluorescence staining. Apoptosis and oxidative stress were evaluated by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining and reactive oxygen species (ROS). Inflammation, apoptosis, oxidative stress, and related pathway protein expression were studied by western blotting. In addition, the levels of CD3 and CD28 proteins were measured by flow cytometry. In the current study, we found that CD28 deficiency significantly inhibited blast exposure-induced increases in the lung weight/body weight ratio and wet weight/dry weight ratio; decreased the infiltration of CD44+ leukocytes, CD163+ macrophages, and CD3+ T cells into the lungs; reduced the expressions of proinflammatory cytokines including IL-1β, TNF-α, and IL-6; and markedly increased IL-10 expression. CD28 deficiency also significantly attenuated blast exposure-induced ROS, MDA5, and IREα expressions; increased SOD-1 expression; lowered the number of apoptotic cells and Bax, Caspase-3, and active Caspase-8 expressions; and increased Bcl-2 expression. Additionally, CD28 deficiency significantly ameliorated blast exposure-induced increases of p-PI3K and p-Akt and ameliorated the decrease in the p-FoxO1 expression. Our results suggest that CD28 deficiency has a protective effect on blast exposure-induced lung injury, which might be associated with the PI3K/Akt/FoxO1 signaling pathway.
EXP1 is required for organization of the intraerythrocytic malaria parasite vacuole

Intraerythrocytic malaria parasites reside within a parasitophorous vacuole membrane (PVM) that closely overlays the parasite plasma membrane (PPM) and constitutes the barrier between parasite and host compartments. The PVM is the site of several essential transport activities but the basis for organization of this membrane system is unknown. We utilized the second-generation promiscuous biotin ligase BioID2 fused to EXP2 or HSP101 to probe the content of the PVM, identifying known and novel candidate PVM proteins. Among the best represented hits were members of a group of single-pass integral membrane proteins that constitute a major component of the PVM proteome but whose function remains unclear. We investigated the function of EXP1, the longest known member of this group, by adapting a CRISPR/Cpf1 genome editing system to install the TetR-DOZI-aptamers system for conditional translational control. EXP1 knockdown was essential for intraerythrocytic development and accompanied by profound changes in vacuole ultrastructure, including increased separation of the PVM and PPM and formation of abnormal membrane structures in the enlarged vacuole lumen. While previous in vitro studies indicated EXP1 possesses glutathione S-transferase activity, a mutant version of EXP1 lacking a residue important for this activity in vitro still provides substantial rescue of endogenous exp1 knockdown in vivo. Intriguingly, while activity of the Plasmodium translocon of exported proteins was not impacted by depletion of EXP1, the distribution of the translocon pore-forming protein EXP2 was substantially altered. Collectively, our results reveal a novel PVM defect that indicates a critical role for EXP1 in maintaining proper PVM organization. Importance Like other obligate intracellular apicomplexans, blood-stage malaria parasites reside within a membrane-bound compartment inside the erythrocyte known as the parasitophorous vacuole. Although the vacuole is the site of several transport activities essential to parasite survival, little is known about its organization. To explore vacuole biology, we adopted recently developed proteomic (BioID2) and genetic (CRISPR/Cpf1) tools for use in Plasmodium falciparum, which allowed us to query the function of the prototypical vacuole membrane protein EXP1. Knockdown of EXP1 showed that a previously reported glutathione S-transferase activity cannot fully account for the essential function(s) of EXP1 and revealed a novel role for this protein in maintaining normal vacuole morphology and PVM protein arrangement. Our results provide new insight into vacuole organization and illustrate the power of BioID2 and Cpf1 (which utilizes a T-rich PAM uniquely suited to the P. falciparum genome) for proximity protein identification and genome editing in P. falciparum.
Effects of Soybean Meal Fermented by Lactobacillus Species and Clostridium butyricum on Growth Performance, Diarrhea Incidence, and Fecal Bacteria in Weaning Piglets

Abstract Fermented soybean meal (FSBM) has been widely investigated as a nutritional strategy for reducing the use of fish meal (FM) and antibiotic growth promoters. Microbial fermentation by using bacteria can increase the bioavailability of nutrients and reduce the levels of antinutritional factors in soybean meal (SBM). In this study, we evaluated whether FSBM produced from Lactobacillus species and Clostridium butyricum improves growth performance, diarrhea incidence, and fecal bacteria in weaning piglets. Eighty-four crossbred male piglets with an average initial body weight of 8.36±0.63 kg were randomly allotted to 3 dietary treatments consisting of 7 replicate stalls with 4 piglets each. The dietary treatments were: (1) 3% FM in the diet; (2) 5% FSBM in the diet; and (3) 3% FM in the diet plus 4 mg/kg antibiotic growth promoters (AGP). We determined that growth performance was unaffected in FSBM-fed weaning piglets compared with a FM group. Similar to the AGP group, FSBM supplementation significantly reduced diarrhea incidence in weaning piglets. The number of fecal Lactobacillus species significantly increased in 28-day-old FSBM-fed weaning piglets compared with the other groups. Compared with AGP, FSBM has the highest inhibitory effect on the number of fecal Enterobacteriaceae at 28 d old. Furthermore, serum immunoglobulin G and immunoglobulin A levels in FSBM-fed weaning piglets significantly increased at the same age. These results together indicate that FSBM can replace FM in the diets of weaning piglets without affecting growth performance. Furthermore, similar to AGP, FSBM could improve diarrhea incidence, fecal bacteria, and immunoglobulin levels in weaning piglets. Therefore, SBM fermented by Lactobacillus species and C. butyricum demonstrated high potential for development as swine feed ingredients.
Seromonitoring of Peste des Petits Ruminants in goats and molecular characterization of PPR virus from field cases

Objectives: The study was undertaken with the objectives to perform seromonitoring of Peste des Petits Ruminants (PPR) antibodies in goats vaccinated with PPR vaccine and molecular characterization of PPR virus (PPRV) from field cases in Bangladesh. Materials and Methods: Seromonitoring work was conducted in Char Kalibari, Mymensingh Sadar, Mymensingh. For this, a total of 50 goats were randomly selected and were divided into two groups; vaccinated (Group A; n = 25) and non-vaccinated (Group B; n = 25). The goats of both groups were again sub-divided into four age groups; (i) 0–6 months (n = 5), (ii) 6–12 months (n = 5), (iii) 12–24 months (n = 10), and (iv) >24 months (n = 5). Blood samples were collected on Day-0 and after 21 days of post-vaccination (DPV), and the sera were prepared. The sera were examined for the presence of antibodies against PPRV by competitive enzyme-linked immunosorbent assay. For molecular characterization, nasal swabs (n = 10) were collected from PPR infected goats in Jessore during PPR outbreak (February 2016). The causative agent, PPRV isolated from field cases were confirmed by N gene based on reverse transcription polymerase chain reaction (RT-PCR), followed by sequencing, phylogenetic analysis, and multiple sequence alignment analyses. Results: In the case of seromonitoring, the results revealed that before vaccination (at Day-0), overall, 44% (n = 22/50) goats were seropositive for PPRV. In Group A, 48% (n = 12/25) goats were seropositive, but after 21 DPV, 96% (n = 24/25) goats become seropositive. On the other hand, in Group B, 40% (n = 10/25) and 16% (n = 04/25) seropositive goats found at Day-0 and after 21 DPV, respectively, indicating that the antibody titer was increasing after vaccination and decreasing in convalescent goats. Out of 10 nasal swab samples, 40% (n = 4/10) was confirmed by RT-PCR targeting nucleocapsid (N gene). Phylogenetically, our isolate (KY039156/PPRV/BDG/Jes/2016) was similar to the other strains of PPRV under lineage IV. However, there was a unique amino acid substitution, where glycine (G) was recorded in place of arginine (R). The strain is closely related with other Chinese or Indian strains. The nucleotide sequence homology by NCBI BLAST search of the isolated strain ranged from 95% to 99% with other strains circulating in Bangladesh. Conclusion: The PPRV is prevailing in the Mymensingh and Jessore regions of Bangladesh. Effective control of PPR in goats may depend on vaccination with PPR vaccine. Molecular characterization of PPRV in Jessore reveals that the virus is differing from the strain prevalent in other regions of Bangladesh and the world.
Influence of environmental variables and human activities on the seasonal habitat use by guanacos in Southern Andean Precordillera (Argentina)

ABSTRACT Food availability, predation risk, climatic adversity, and human disturbance are usually considered relevant factors influencing the distribution of wild ungulates. Poaching and habitat degradation are threats to the guanaco, a native herbivore of South America characterized by ecological and behavioral adaptations to arid environments. Guanaco presence was seasonally surveyed in mountain environments of Andean Precordillera, corresponding to a protected area and its surroundings. Field surveys and satellite images processing estimated environmental variables ascribed to four predictions: resources availability, habitat complexity, weather conditions, and human activities. Generalized Linear Models estimated the probability of guanaco presence based on each prediction, whose variables with important effect were included in combined models. The main natural influence on the presence of guanaco was plant cover. Conservation activities improved this natural influence, whereas disturbing activities restricted it. The trade-off between high resources availability and low predation risk, as well as the effect of extreme weather conditions were not evident, at least in the study’s spatial scale. The model validation with new seasonal surveys confirmed a consistency over time of those environmental variables that explain the probability of guanaco presence in the Southern Andean Precordillera.
Salmon lice sampled from wild Atlantic salmon and sea trout throughout Norway display high frequencies of the genotype associated with pyrethroid resistance

Atlantic salmon Salmo salar aquaculture is based on the use of open-pen sea cages, with the consequence that farmed fish are both recipients and sources of pathogens from surrounding waters. Currently, the parasitic salmon louse Lepeophtheirus salmonis represents the most critical biological challenge for salmonid aquaculture in the Atlantic Ocean. This has, in part, been driven by the emergence of resistance to the few delousing agents available to the industry. In the present study, we investigated resistance to pyrethroids. Lice sampled in 2014 from wild Atlantic salmon and sea trout Salmo trutta hosts from Norway were genotyped using the genetic marker associated with pyrethroid resistance and compared to data from lice sampled on farmed hosts in the same regions and period. The resistant genotype was observed in lice from both wild hosts in all regions of Norway. In all regions, frequencies of the resistant genotype were similar for lice from sea trout and farmed salmon, approaching fixation in some areas. In most regions, lice from wild salmon displayed lower frequencies of the resistant genotype than lice from both wild sea trout and farmed salmon. Lice are only directly exposed to chemical selection within aquaculture. Therefore, these data demonstrate an extensive gene flow and exchange of lice between farmed and wild salmonid hosts. It is also suggested that the observed lower frequency of the resistant genotype in lice from wild salmon returning to the coast is due to a dilution effect mediated by infestation with lice originating from outside farming areas while in the oceanic feeding grounds.