Miracle-dz/UniFAR-FTUs huggingface dataset:
zGrad: A nanobody-based degron system to inactivate proteins in zebrafish

The analysis of protein function is essential to modern biology. While protein function has mostly been studied through gene or RNA interference, more recent approaches to degrade proteins directly have been developed. Here, we adapted the anti-GFP nanobody-based system deGradFP from flies to zebrafish. We named this system zGrad and show that zGrad efficiently degrades transmembrane, cytosolic and nuclear GFP-tagged proteins in zebrafish in an inducible and reversible manner. Using tissue-specific and inducible promoters in combination with functional GFP-fusion proteins, we demonstrate that zGrad can inactivate transmembrane, cytosolic and nuclear proteins globally, locally and temporally with different consequences. Global protein depletion results in phenotypes similar to loss of gene activity while local and temporal protein inactivation yields more restricted and novel phenotypes. Thus, zGrad is a versatile tool to study the spatial and temporal requirement of proteins in zebrafish.
Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization

Abstract Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open‐source UCE probe set for beetles of the suborder Adephaga.
Mechanoreceptor-mediated circuit regulates cold tolerance in Caenorhabditis elegans

C. elegans mechanoreceptors located in the ASG sensoryneuron have been found to sense temperature — a key trait for animal survival. Experimental loss of xanthine dehydrogenase (XDH-1) function in the AIN and AVJ interneurons resulted in reduced cold tolerance and atypical neuronal response to changes in temperature. These interneurons are synapse with upstream neurons such as the mechanoreceptor-expressing ASG. Ca2+ imaging revealed that ASG responsiveness to temperature change via mechanoreceptor DEG-1, a Degenerin/Epithelial Sodium Channel (DEG/ENaC), affects downstream AIN and AVJ circuits. Ectopic expression of DEG-1 in the ASE gustatory neuron resulted in acquisition of thermosensitivity, while electrophysiological analysis revealed that DEG-1 was involved in temperature sensation. Together, these results suggest that cold tolerance is regulated by mechanoreceptor-mediated circuit calculation.
Lytic Bacteriophages and Phage Cocktails Seem to be a Future Alternative Against Multi-Drug Resistant Bacterial Infections

Lytic bacteriophages have the efficacy to act and eradicate pathogenic bacteria as an attractive tool in the near future. Bacteriophages specifically kill multidrug-resistant bacteria even which have the capacity to form biofilms. The present review mainly focused on the efficacy of bacteriophages and cocktails as therapeutic agents against predominate MDR-bacteria and their biofilms which are isolated from septic wound infections. The body of evidence includes data from studies investigating bacteriophages from sewage samples as novel antibacterial and antibiofilm agents against pathogenic bacteria. The goal of this review is to present an overview on predominant bacteria from septic wound infection, the biofilm-forming capacity of bacteria, lytic effect of bacteriophages and phage cocktails with an emphasis on the application of bacteriophages against septic wound causing bacteria.
A New Species of Acalypha L. (Euphorbiaceae) from the Brazilian Atlantic Rain Forest

Abstract As part of taxonomic studies of the genus Acalypha in eastern Brazil, we describe here a new species, Acalypha almadinensis, from the Atlantic Rain Forest, in the states of Bahia and Minas Gerais. This species is morphologically similar to Acalypha brasiliensis and A. accedens, but differs from both mainly by its fleshy pistillate bracts and vinaceous lower leaf surface.
The Genomic Impact of European Colonization of the Americas

The human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored. Here we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased gene-flow dynamics, of the Americas. We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.
Smart Surveillance Camera of Detection Human

The Surveillance camera problem in detection human and car remove noise, find object quickly. In orginal algorithm using different of frame or find curve to detection human. Surveillance camera system in illumination problem is very challenge task. Illumination and environment light is change object reflecting energy. From start using surveillance camera their system has many problems, wind change camera pose, cloud, illumination condition, cat and dog all these noise from surveillance camera is moving object because the camera field of view these object is change background. These problems for all automatic surveillance system detection object of interest in input scene. Common algorithm is for segmentation of moving object is DOF( Different of Frame) background subtraction. But all these algorithm not enough to find human accuracy. Early times HOG algorithm is need long computing time. GPU(graphic process unit) can support it to real time detection human and car.
When does extreme drought elicit extreme ecological responses?

Global climate change models predict an increase in the frequency and intensity of extreme droughts, with uncertain ecological impacts across ecosystems. In particular, it is not clear when extreme droughts will elicit extreme ecological responses. For this study, we employed three complementary approaches to explore the relationships between extreme drought and ecosystem responses. First, we used global data mining to evaluate the relationship between extreme gross primary productivity and extreme precipitation from 1980 to 2013. Second, we conducted a meta‐analysis using 132 drought experiments across the globe to assess the response ratios (RRs) of above‐ground net primary productivity (ANPP) to extreme versus non‐extreme drought treatments. Third, we examined community and ecosystem responses in an alpine meadow to a drought gradient experiment, which included five precipitation treatment levels (1/12 P, 1/4 P, 1/2 P, 3/4 P, and P, where P is the growing season precipitation). This study had three key results. In our historical data mining, we found that extreme droughts elicited extreme ecological responses only 15.1% of the time. The meta‐analysis results indicated that there were no significant differences in the RRs of ANPP between the extreme versus non‐extreme drought treatments. The drought gradient experiment results revealed that although the four drought treatments were statistically extreme, only the most extreme drought treatment (1/12 P) significantly reduced ANPP over the 3 years. Meanwhile, species richness and asynchrony were significantly reduced under the 1/12 P treatment, which led to a significant reduction in productivity. Synthesis. These results suggest that extreme ecological responses to extreme drought may be less frequent than previously thought. But when they do occur, extreme ecological responses may be driven by plant community changes such as species asynchrony, species loss or species reordering. Our experimental results highlight the key role of community dynamics in determining the resistance of ecosystem productivity to extreme drought, which should be assessed when predicting ecological responses to climate change.
Modeling of Full Electric and Hybrid Electric Vehicles

Full Electrical Vehicles (FEVs) and Hybrid Electrical Vehicles (HEVs) are vehicles with many electric components compared to conventional ones. In fact the power train consists of electrical machines, power electronics and electric energy storage system (battery, super capacitors) connected to mechanical components (transmissions, gear boxes and wheels) and, for HEV, to an Internal Combustion Engine (ICE). The approach for a new vehicle design has to be multidisciplinary in order to take into account the dynamic interaction among all the components of the vehicle and the power train itself. The vehicle designers in order to find the correct sizing of components, the best energy control strategy and to minimize the vehicle energy consumption need modeling and simulation since prototyping and testing are expensive and complex operations. Developing a simulation model with a sufficient level of accuracy for all the different components based on different physic domains (electric, mechanical, thermal, power electronic, electrochemical and control) is a challenge. Different commercial simulation tools have been proposed in literature and they are used by the automotive designer [1]. They have different level of detail and are based on different mathematical approaches. In paragraph 2 a general overview on different modeling approaches will be presented. In the following paragraphs the author approach, focused on the modeling of each component constituting a FEV or HEV will be detailed. The authors approach is general and is not based on vehicle oriented simulation tools. It represents a good compromise among model simplicity, flexibility, computational load and components detail representation. The chapter is organized as follows:
A non-canonical role for dynamin-1 in regulating early stages of clathrin-mediated endocytosis in non-neuronal cells

Dynamin GTPases are best studied for their role in the terminal membrane fission process of clathrin-mediated endocytosis (CME); but, they have also been proposed to regulate earlier stages of CME. Although highly enriched in neurons, dynamin-1 (Dyn1) is, in fact, widely expressed along with dynamin-2 (Dyn2), but inactivated in non-neuronal cells via phosphorylation by GSK3β kinase. Here, we study the differential, isoform-specific functions of Dyn1 and Dyn2 as regulators of CME. Endogenously expressed Dyn1 and Dyn2 were fluorescently-tagged either separately or together in two cell lines with contrasting Dyn1 expression levels. By quantitative live cell dual and triple-channel total internal reflection fluorescence microscopy we find that Dyn2 is more efficiently recruited to clathrin-coated pits (CCPs) than Dyn1, and that Dyn2, but not Dyn1 exhibits a burst of assembly prior to CCV formation. Activation of Dyn1 by acute inhibition of GSK3β results in more rapid endocytosis of transferrin receptors, increased rates of CCP initiation and decreased CCP lifetimes, but did not significantly affect the extent of Dyn1 recruitment to CCPs. Thus, activated Dyn1 can regulate early stages of CME even when present at low, substoichiometric levels relative to Dyn2, and apparently without assembly into supramolecular collar-like structures. Under physiological conditions Dyn1 is activated downstream of EGF-receptor signaling to alter CCP dynamics. We identify sorting nexin 9 (SNX9) as a preferred binding partner to activated Dyn1 that is partially required for Dyn1-dependent effects on early stages of CCP maturation. Together, we decouple regulatory and scission functions of dynamins and report a scission-independent, isoformspecific regulatory role for Dyn1 in clathrin-mediated endocytosis.
Grouping patterns and social organization in Siberian ibex (Capra sibirica): feeding strategy matters

Abstract. A study on group size and composition in Siberian ibex (Capra sibirica) was conducted in the Eastern Tien-Shan Mountains. We found that small groups (1-5 individuals) were most common for this species. Generally, mixed-sex groups were larger than male and female groups. Since males have more ability for fiber digestion, because of their larger body size than females, they are less selective in food quality. Due to this, males gathered into larger single-sex groups in August-September, when forage was at its maximal biomass, and into smaller groups when the amount of food was limited (winter-early-spring). During birthing period, pregnant females typically separated from groups to give birth, returning to the female groups in May-June, when high-quality food was at its maximal availability, making female groups largest in this period. Similar to other sexually dimorphic species, Siberian ibex females and males stayed together in mixed-sex groups during rutting season, demonstrating sexual segregation outside of the rutting season, particularly during summer. Nevertheless, there are still a significant number of males and females that stay in mixed-sex groups throughout the year. In conclusion, the grouping pattern and social organization of Siberian ibex were closely correlated to the availability and quality of their food supply and yearly breeding cycle. Accordingly, Siberian ibexes changed their feeding strategy: being mixed feeders they behaved similar to concentrate selectors when food was scant and preferred small sized groups; while they enlarged their group sizes during seasons when the enriching of forage conditions allowed them to do that. However, group enlarging happened in different months depending on group typology (i.e. mixed-sex, male or female groups) depending on the feeding strategy of their individuals.
Quorum sensing: A molecular cell communication in bacterial cells

Background: Quorum sensing is a cell-to-cell communication, which is extensively observed in bacteria. This process allows the cell to detect, analyze, share and act upon various environmental stimuli based on cell density. The molecular aspect of this process is the secretion and detection of chemical signaling molecules called autoinducers (AIs), which act upon the gene expression. The quorum sensing signaling pathway is specifically observed only bulk population or in other words, the quorum sensing is effective only in high cell density. The quorum sensing circuit in the bacterial population is widely studied under the following heading; quorum sensing in Gram positive bacterium, Quorum sensing in Gram negative bacterium and the Quorum sensing with respect to Interkingdom communication. These models are studied using the widely studied models like Vibrio fischeri in Gram negative QS circuit, Staphylococcus aureus in Gram positive QS circuit and Vibrio harveyi. This review paper details the introduction of quorum sensing and their gene level explanation and how they effect on the virulence of a particular species of bacteria. This paper also throws light on the realization that the bacteria has the capable of performing coordinated activities that was so long contributed to the eukaryotic cell performance.
Clutter Reduction in Parallel Coordinates using Binning Approach for Improved Visualization

As the data and number of information sources keeps on mounting, the mining of necessary information and their presentation in a human delicate form becomes a great challenge. Visualization helps us to pictorially represent, evaluate and uncover the knowledge from the data under consideration. Data visualization offers its immense opportunity in the fields of trade, banking, finance, insurance, energy etc. With the data explosion in various fields, there is a large importance for visualization techniques. But when the quantity of data becomes elevated, the visualization methods may take away the competency. Parallel coordinates is an eminent and often used method for data visualization. However the efficiency of this method will be abridged if there are large amount of instances in the dataset, thereby making the visualization clumsier and the data retrieval very inefficient. Here we introduced a data summarization approach as a preprocessing step to the existing parallel coordinate method to make the visualization more proficient.
PARP1 as a biomarker for early detection and intraoperative tumor delineation in epithelial cancers – first-in-human results

Major determining factors for survival of patients with oral, oropharyngeal, and esophageal cancer are early detection, the quality of surgical margins, and the contemporaneous detection of residual tumor. Intuitively, the exposed location at the epithelial surface qualifies these tumor types for utilization of visual aids to assist in discriminating tumor from healthy surrounding tissue. Here, we explored the DNA repair enzyme PARP1 as imaging biomarker and conducted optical imaging in animal models, human tissues and as part of a first-in-human clinical trial. Our data suggests that PARP1 is a quantitative biomarker for oral, oropharyngeal, and esophageal cancer and can be visualized with PARPi-FL, a fluorescently labeled small molecule contrast agent for topical or intravenous delivery. We show feasibility of PARPi-FL-assisted tumor detection in esophageal cancer, oropharyngeal and oral cancer. We developed a contemporaneous PARPi-FL topical staining protocol for human biospecimens. Using fresh oral cancer tissues within 25 min of biopsy, tumor and margin samples were correctly identified with >95% sensitivity and specificity without terminal processing. PARPi-FL imaging can be integrated into clinical workflows, potentially providing instantaneous assessment of the presence or absence of microscopic disease at the surgical margin. Additionally, we showed first-in-human PARPi-FL imaging in oral cancer. In aggregate, our preclinical and clinical studies have the unifying goal of verifying the clinical value of PARPi-FL-based optical imaging for early detection and intraoperative margin assignment.
Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae

Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped specialized metabolite diversity, which drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating specialized metabolite diversity in an evolutionary context have been limited by the impossibility to identify chemical structures of hundreds to thousands of compounds in a time-feasible manner. Here, we introduce a workflow for large-scale, semi-automated annotation of specialized metabolites, and apply it for over 1000 metabolites of the cosmopolitan plant family Rhamnaceae. We enhance the putative annotation coverage dramatically, from 2.5 % based on spectral library matches alone to 42.6 % of total MS/MS molecular features extending annotations from well-known plant compound classes into the dark plant metabolomics matter. To gain insights in substructural diversity within the plant family, we also extract patterns of co-occurring fragments and neutral losses, so-called Mass2Motifs, from the dataset; for example, only the Ziziphoid clade developed the triterpenoid biosynthetic pathway, whereas the Rhamnoid clade predominantly developed diversity in flavonoid glycosides, including 7-O-methyltransferase activity. Our workflow provides the foundations towards the automated, high-throughput chemical identification of massive metabolite spaces, and we expect it to revolutionize our understanding of plant chemoevolutionary mechanisms.
Genetic variability of tambaqui broodstocks in the Brazilian state of Pará

ABSTRACT The present study evaluated the genetic variability of the broodstocks of tambaqui hatcheries in the Brazilian state of Para. Samples were obtained from the caudal fin of 110 broodstocks from one hatchery in each of four municipalities (Santarem, Peixe-Boi, Breu-Branco, and Ulianopolis), representing all the individuals of each hatchery stock. The samples were genotyped using the multiplex system microsatellite markers. Data were used to calculate observed and expected heterozygosity, number of alleles per locus, and allelic richness. The effective [. ]
Effects of various Toxeat concentrations on growth performance, immune response, cecal microflora, and gut morphology in broilers fed with aflatoxin contaminated diets

Soheila SARRAMI, Parvaneh JAFARI*, Maryam TAJABADI EBRAHIMI, Seyed Naser MOUSAVI, Seyed Abdollah HOSSEINI Department of Microbiology, Faculty of Science, Islamic Azad University, Arak Branch, Arak, Iran Department of Biology, Faculty of Science, Islamic Azad University, Central Tehran Branch,Tehran, Iran Department of Animal Science, Islamic Azad University, Varamin-Pishva Branch,Varamin, Iran Department of Animal Nutrition and Physiology, Animal Science Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
Activation and Antagonism of RIG-I-Mediated Innate Immune Signaling by Herpes Simplex Virus 1

The cytosolic innate immune receptor retinoic acid-inducible gene-I (RIG-I) recognizes double-stranded RNA (dsRNA) that emerges during viral infection and initiates an antiviral response comprised of interferon (IFN) and proinflammatory cytokine induction. Although RIG-I plays a role in the immune response to DNA viruses such as herpes simplex virus 1 (HSV-1), little is known about the nature of RNA ligands that activate RIG-I during DNA virus infection, and moreover, how these viruses antagonize RIG-I signaling. To identify physiological RNA ligands of RIG-I during HSV-1 infection, we performed RNA-Seq on RIG-I-bound RNA from HSV-1-infected cells and found that the 5S rRNA pseudogene RNA5SP141 was highly enriched with RIG-I specifically in infected cells and elicited a robust RIG-I-dependent antiviral response. In uninfected cells, RNA5SP141 is found primarily in the nucleus, but upon HSV-1 infection, its localization becomes predominantly cytoplasmic. Furthermore, HSV-1-induced shutoff of host protein expression results in the downregulation of proteins that normally interact with and shield RNA5SP141 from RIG-I detection. Depletion of endogenous RNA5SP141 strongly dampened the antiviral response to HSV-1 and the related Epstein-Barr virus, as well as influenza A virus, an RNA virus. Taken together, our data show that viral infection can lead to deshielding of endogenous RNAs that activate innate immunity.