Miracle-dz/UniFAR-FTUs huggingface dataset:
NSP 11 of SARS-CoV-2 is an Intrinsically Disordered Protein

The intrinsically disordered proteins/regions (IDPs/IDPRs) are known to be responsible for multiple cellular processes and are associated with many chronic diseases. In viruses, the existence of disordered proteome is also proven and are related with its conformational dynamics inside the host. The SARS-CoV-2 virus has a large proteome, in which, structure and functions of many proteins are not known as of yet. Previously, we have investigated the dark proteome of SARS-CoV-2. However, the disorder status of non-structural protein 11 (nsp11) was not possible because of very small in size, just 13 amino acid long, and for most of the IDP predictors, the protein size should be at least 30 amino acid long. Also, the structural dynamics and function status of nsp11 was not known. Hence, we have performed extensive experimentation on nsp11. Our results, based on the Circular dichroism spectroscopy gives characteristic disordered spectrum for IDPs. Further, we investigated the conformational behaviour of nsp11 in the presence of membrane mimetic environment, alpha helix inducer, and natural osmolyte. In the presence of negatively charged and neutral liposomes, nsp11 remains disordered. However, with SDS micelle, it adopted an α-helical conformation, suggesting the helical propensity of nsp11. At the end, we again confirmed the IDP behaviour of nsp11 using molecular dynamics simulations.
Targeting hypoxic habitats with hypoxia pro-drug evofosfamide in preclinical models of sarcoma

Hypoxic regions (habitats) within tumors are heterogeneously distributed and can be widely variant. Hypoxic habitats are generally pan-therapy resistant. For this reason, hypoxia-activated prodrugs (HAPs) have been developed to target these resistant volumes. The HAP evofosfamide (TH-302) has shown promise in preclinical and early clinical trials of sarcoma. However, in a phase III clinical trial, TH-302 did not improve survival in combination with doxorubicin (dox), most likely due to a lack of patient stratification based on hypoxic status. Herein, our goal was to develop deep-learning (DL) models to identify hypoxic habitats, using multiparametric (mp) MRI and co-registered histology, and to non-invasively monitor response to TH-302 in a patient-derived xenograft (PDX) of rhabdomyosarcoma and a syngeneic model of fibrosarcoma (RIF-1). A DL convolutional neural network showed strong correlations (>0.81) between the true hypoxic portion in histology and the predicted hypoxic portion in multiparametric MRI. TH-302 monotherapy or in combination with Dox delayed tumor growth and increased survival in the hypoxic PDX model (p<0.05), but not in the RIF-1 model, which had lower volume of hypoxic habitats. Control studies showed that RIF-1 resistance was due to hypoxia and not to other causes. Notably, PDX tumors developed resistance to TH-302 under prolonged treatment. In conclusion, response to TH-302 can be attributed to differences in hypoxia status prior therapy. Development of non-invasive MR imaging to assess hypoxia is crucial in determining the effectiveness of TH-302 therapy and to follow response. In further studies, our approach can be used to better plan therapeutic schedules to avoid resistance. One Sentence Summary Development of non-invasive MR imaging to assess hypoxia is crucial in determining the effectiveness of TH-302 therapy and to follow response.
Quantitation analysis by flow cytometry shows that Wt1 is required for development of the proepicardium and epicardium

The epicardium is a cell layer found on the external surface of the heart. During development it has an epithelial identity and contains progenitor cells for coronary smooth muscle and cardiac fibroblasts. The epicardium has been suggested to have therapeutic potential in cardiac repair. Study of epicardial development has been difficult because it is dynamic and morphologically complex. We developed a flow cytometry-based method to quantify cardiac development including the epicardial lineage. This provided accurate and sensitive analysis of (1) the emergence of epicardial progenitors within the proepicardium (2) their transfer to the heart to form the epicardium, and (3) their epithelial-to-mesenchymal transition (EMT) to create the subepicardium. Platelet-derived growth factor alpha (Pdgfra) and Wilms tumor protein (Wt1) have both been reported to be pro-mesenchymal during epicardial EMT. Quantitative analysis with flow cytometry confirmed a pro-mesenchymal role for Pdgfra but not for Wt1. Analysis of Wt1 null embryos showed that they had (1) poor formation of proepicardial villi, (2) reduced transfer of proepicardial cells to the heart, (3) a discontinuous epicardium with poor epithelial identity, and (4) a proportionally excessive number of mesenchymal-like cells. This data shows that Wt1 is essential for epicardial formation and maintenance rather than being pro-mesenchymal.
SepF is the FtsZ-anchor in Archaea: implications for cell division in the Last Universal Common Ancestor

The Archaea present profound differences compared to Bacteria in fundamental molecular and cellular processes. While most Archaea divide by binary fission using an FtsZ-based system similar to Bacteria, they lack the majority of the components forming the complex bacterial divisome. Moreover, how FtsZ precisely functions and interacts with other proteins to assemble the archaeal division machinery remains largely unknown. Notably, among the multiple bacterial factors that tether FtsZ to the membrane during cell constriction, Archaea only possess SepF-like homologues, but their function has not been demonstrated. Here, we combine structural, cellular, and evolutionary approaches to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy of immunolabeled cells shows that M. smithii SepF co-localizes with FtsZ at the division plane. We also show that M. smithii SepF binds both to membranes and FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with FtsZCTD reveal that SepF forms a dimer with a specific homodimerization interface. This drives a strikingly different binding mode from what is observed in Bacteria. Finally, analysis of the distribution and phylogeny of SepF and FtsZ indicates that these proteins date back to the Last Universal Common Ancestor (LUCA) and that Archaea may have retained features of an ancestral minimal cell division system, while Bacteria likely diverged to accommodate the emergence of the complex machinery required to coordinate cytokinesis with the rigid peptidoglycan cell wall and the appearance of additional FtsZ tethers. Our results contribute key insights into the largely understudied mechanisms of archaeal cell division, and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.
Crumbs and the apical spectrin cytoskeleton regulate R8 cell fate in the Drosophila eye

The Hippo pathway is an important regulator of organ growth and cell fate. In the R8 photoreceptor cells of the Drosophila melanogaster eye, the Hippo pathway controls the fate choice between one of two subtypes that express either the blue light-sensitive Rhodopsin 5 (Hippo inactive) or the green light-sensitive Rhodopsin 6 (Hippo active). The degree to which the mechanism of Hippo signal transduction and the proteins that mediate it are conserved in organ growth and R8 cell fate choice is currently unclear. Here, we identify Crumbs and the apical spectrin cytoskeleton as regulators of R8 cell fate. By contrast, other proteins that influence Hippo-dependent organ growth, such as the basolateral spectrin cytoskeleton and Ajuba, are dispensable for the R8 cell fate choice. Surprisingly, Crumbs promotes the Rhodopsin 5 cell fate, which is driven by Yorkie, rather than the Rhodopsin 6 cell fate, which is driven by Warts and the Hippo pathway, which contrasts with its impact on Hippo activity in organ growth. Furthermore, neither the apical spectrin cytoskeleton nor Crumbs regulate the Hippo pathway through mechanisms that have been reported to operate in growing organs. Together, these results show that only a subset of Hippo pathway proteins regulate the R8 binary cell fate decision and that aspects of Hippo pathway signalling appear to differ between growing organs and post-mitotic R8 cells.
Genetic population subdivision of Blue Swimming Crab (Portunus pelagicus) across Indonesia inferred from mitochondrial DNA: implication to sustainable fishery

The blue swimming crab (BSC), Portunus pelagicus (Linnaeus 1758), inhabits coastal areas of Southeast and East Asia, and is one of high fisheries commodity with export value for Indonesia and global market demand increasing annually. However, the data of genetic diversity and their spatial connectivity of populations in Indonesia are not yet known, which is important to inform unit stock management and sustainable fisheries. This study aimed to determine genetic diversity and differentiation of blue swimming crab across Indonesia populations under different Fishery Management Area, and their spatial genetic connectivity, as well as implications for sustainable fishery. A total of 297 individuals were amplified using cytochrome oxidase I mitochondrial DNA. This study shown highest value of haplotype and nucleotide diversity in the eastern part of Indonesia, where exploitation is relatively low. Significant genetic differentiation between populations (FST = 0.954; p < 0.001) and the fishery management regions (FST = 0.964; p < 0.001) were revealed. Low spatial connectivity was observed between populations in a distance of at least more than 60 kilometers. This study suggests that BSC populations in Indonesia likely have several unit stock, and preferably different fisheries management plan and action across the region thoroughly and simultaneously is effective for management and their sustainable conservation.
Chicken cGAS Senses Fowlpox Virus Infection and Regulates Macrophage Effector Functions

The anti-viral immune response is dependent on the ability of infected cells to sense foreign nucleic acids. In multiple species, the pattern recognition receptor (PRR) cyclic GMP-AMP synthase (cGAS) senses viral DNA as an essential component of the innate response. cGAS initiates a range of signalling outputs that are dependent on generation of the second messenger cGAMP that binds to the adaptor protein stimulator of interferon genes (STING). Here we show that in chicken macrophages, the cGAS/STING pathway is essential not only for the production of type-I interferons in response to intracellular DNA stimulation, but also for regulation of macrophage effector functions including the expression of MHC-II and co-stimulatory molecules. In the context of fowlpox, an avian DNA virus infection, the cGAS/STING pathway was found to be responsible for type-I interferon production and MHC-II transcription. The sensing of fowlpox virus DNA is therefore essential for mounting an anti-viral response in chicken cells and for regulation of a specific set of macrophage effector functions.
Epistasis, aneuploidy, and gain-of-function mutations underlie the evolution of resistance to induced microtubule depolymerization

Microtubules, polymers of alpha- and beta-tubulin, are essential cellular components. When microtubule polymerization is hindered, cells are delayed in mitosis, but eventually they manage to proliferate with massive chromosome missegregation. Several studies have analyzed the first cell division upon microtubules impairing conditions. Here, we asked how cells cope on the long term. Taking advantage of mutations in beta-tubulin, we evolved in the lab for ∼150 generations 24 populations of yeast cells unable to properly polymerize microtubules. At the end of the evolution experiment, cells re-gained the ability to form microtubules, and were less sensitive to microtubule depolymerizing drugs. Whole genome sequencing allowed us to identify genes recurrently mutated (tubulins and kinesins) as well as the pervasive duplication of chromosome VIII. We confirmed that mutations found in these genes and disomy of chromosome VIII allow cells to compensate for the original mutation in beta-tubulin. The mutations we identified were mostly gain-of-function, likely re-allowing the proper use of the mutated form of beta-tubulin. When we analyzed the temporal order of mutations leading to resistance in independent populations, we observed multiple times the same series of events: disomy of chromosome VIII followed by one additional adaptive mutation in either tubulins or kinesins. Analyzing the epistatic interactions among different mutations, we observed that some mutations benefited from the disomy of chromosome VIII and others did not. Given that tubulins are highly conserved among eukaryotes, our results are potentially relevant for understanding the emergence of resistance to drugs targeting microtubules, widely used for cancer treatment.
Cross-compartment signal propagation in the mitotic exit network

In budding yeast, the Mitotic Exit Network (MEN), a GTPase signaling cascade integrates spatial and temporal cues to promote exit from mitosis. This signal integration requires transmission of a signal generated on the cytoplasmic face of spindle pole bodies (SPBs; yeast equivalent of centrosomes) to the nucleolus, where the MEN effector protein Cdc14 resides. Here, we show that the MEN activating signal at SPBs is relayed to Cdc14 in the nucleolus through the dynamic localization of its terminal kinase complex Dbf2-Mob1. Cdc15, the protein kinase that activates Dbf2-Mob1 at SPBs, also regulates its nuclear access. Once in the nucleus, priming phosphorylation of Cfi1/Net1, the nucleolar anchor of Cdc14, by the Polo-like kinase Cdc5 targets Dbf2-Mob1 to the nucleolus. Nucleolar Dbf2-Mob1 then phosphorylates Cfi1/Net1 and Cdc14, activating Cdc14. The kinase-primed transmission of the MEN signal from the cytoplasm to the nucleolus exemplifies how signaling cascades can bridge distant inputs and responses.
Luxembourg Fund Data Repository

In this paper, we introduce the Luxembourg Fund Data Repository, a novel database of investment funds available for academic research that was created at the Department of Finance of the University of Luxembourg. The database contains the population of Undertakings for Collective Investment in Transferable Securities funds domiciled in Luxembourg from the starting month of their existence (March 1988) to October 2016. The fund characteristics are organized in a comprehensive database architecture encompassing static and dynamic data over the entire life of the funds. The characteristics include fund identifiers, official name, status information, management company and other service providers, daily and monthly performance time-series, portfolio holdings, classification of investment objective, fees, dividends, and cash flows. The database was constructed after collecting and assembling complementary historical information from three data providers. Importantly, funds no longer in existence due to liquidation or mergers are included in the database, preventing survivorship bias. The database has been constructed to serve as a research dataset of high accuracy due to the maximization of population coverage, the maximization of historical coverage, and validation by using information acquired from the supervisory authority of the financial sector of Luxembourg. License currently available to researchers of the Department of Finance of the University of Luxembourg. Future plans for extending accessibility to the global academic community.
SEEDLING GROWTH AND SURVIVAL OF THE ENDANGERED TREE SPECIES SHOREA WANTIANSHUEA AFTER A MAST-FRUITING EVENT

Aims Shorea wantianshuea is an endangered tree species of Dipterocarpaceae in Xishuangbanna seasonal rain forest,and is listed in the Plant Red Book under Grade Ⅰ in China.This species regenerates exclusively from seeds.Our objective was to determine the fate of seedlings(including their growth and survival) following a mast fruiting event.Results will be useful in restoring this species and degraded natural forests dominated by it.Methods In early December 2004,after mast fruiting of S.wantianshuea,we established three parallel 20 m×100 m transects spaced 50 m apart within an area of 100 m×200 m spanning from valley bottom to ridge top.Each transect was stratified into five contiguous plots of 20 m and near the center of each plot two 3 m×3 m quadrats were established.We labeled all newly established S.wantianshuea seedlings in each quadrat,recorded seedling height,basal stem diameter and number of leaves every 2-3 months over a 10-month period and calculated death rate,herbivory rate and survival rate of the seedlings.At the end of the survey,we destructively sampled seedlings and determined leaf areas,total dry weight,root-shoot ratio and specific leaf area.Important findings Many S.wantianshuea seedlings established after the mast-fruiting event did not recruit into its natural population because of high mortality rate and herbivory rate caused by seasonal drought stress,small mammals and other predators.The density of seedlings was as high as 2.76 plants·m-2 in December 2004(first census),but was less than 0.26 plants·m-2 in September 2005 when the study ended.Seedling mortality rate was high during the dry season,particularly after the first two months.The final seedling mortality rate on ridge-top and lower-ridge sites,55% and 54%,respectively,were higher than those on other sites,with a gradually increase from valley bottom to ridge top.Herbivory rate in the first census was low and in 8 of 15 sites no seedlings were gnawed or pulled.At the end of the study,mean seedling height was 17.9,19.7,18.4,13.0 and 12.1 cm in valley-bottom,lower-slope,medium-slope,lower-ridge and ridge-top sites,respectively;however,no significant differences were observed in seedling height and other growth parameters.
Sensitivity of rare minnow (Gobiocypris rarus, IHB) to several common chemicals.

We performed waterborne exposures of several chemicals on adult and embryo-larvae stage rare minnow and compared the sensitivity between the wild group(WG) and closed colony(IHB). Adult rare minnows were acutely exposed to lethal concentrations of the chemical agents(K2Cr2O4, pentachlorophenol, HgCl2, p-Chloroaniline and CdCl2) in order to determine the 96 h LC50(96 h lethal median concentration). For the closed colony, the 96h LC50was 69.0mg/L, 111.4, 56.9 μg/L, 35.5and12. 2mg/L for Cr6+, pentachlorophenol, Hg2+, p-Chloroaniline and Cd2+, respectively. For the wild colony, the 96h LC50was 99.8mg/L, 105.6and 65.8 μg/L for Cr6+, pentachlorophenol, Hg2+, respectively. A significant difference was observed in the exposure to K2Cr2O4between the two colonies(P0.05). Then the embryos(8hours post-fertilization) and larvae(1day post-hatching) from closed colony were exposed to p-Chloroaniline and CdCl2for 7days and the exposure caused toxic effects on hatching, malformation, survival and growth, and among these, growth was the most sensitive parameter to the toxicants stress. For p-Chloroaniline, the obtained none-observable effect concentration(NOEC) for growth were 2and 4mg/L in the embryos and larvae, respectively; while for CdCl2, the NOEC was 0.1mg/L in both the embryos and larvae. Our results suggested that the closed colony rare minnow is sensitive to chemical exposure and can serve as a reliable model organism for testing chemical toxicity.
Protein growth in pigs

Estimates were made of total body protein in 45 unimproved crossbred pigs slaughtered serially between 20 and 200 kg live weight. Allometric functions were used to estimate protein weight at any given body weight and the Gompertz function was used to express live-weight changes in relation to time and to predict weight at maturity. Predicted values for daily protein retention increased rapidly from 20 kg to attain, at around 75 kg live weight, maxima of 130 g for entire males, 120 g for females and 105 g for castrated males. Between 45 and 110 kg live weight rates of protein retention were maintained within 10 g of the maximum rate. Mature live weights were estimated to be 240, 215 and 225 kg for entire males, females and castrated males. The allometric exponents for whole body protein as a function of body weight were 0·963 (s.e. 0·025), 0·927 (s.e. 0·021) and 0·850 (s.e. 0·049) for entire males, females and castrated males respectively.
Molecular Genetics Tools to Understand Foaming and Bulking Filamentous Bacteria in Wastewater Treatment Plants

Water is a critical need not only for human survival, but also for all forms of living organisms and for the conservation of the ecosystems on a global scale. Water contamination is now a major problem in the global context as a consequence of industrialization, globalization, population growth, urbanization and warfare combined with increased wealth and more extravagant lifestyles. Therefore wastewater treatment has gained increased importance worldwide due to increasing demand on fresh clean water supplies.
The role of essential fatty acids on the eicosanoids profile and its impact on immune response.

TÂMARA KELLY DE CASTRO GOMES1; SUZANA LIMA DE OLIVEIRA2 1Mestranda do Programa de Pós-Graduação em Nutrição, Faculdade de Nutrição, Universidade Federal de Alagoas 2Professora da Faculdade de Nutrição, Universidade Federal de Alagoas Endereço para correspondência: Tâmara Kelly de Castro Gomes Conj. Medeiros Neto, bloco 25, apt 303, Tabuleiro dos Martins, Maceió-AL CEP 57060-640. e-mail: tkgomes@gmail.com Local de realização do trabalho: Faculdade de Nutrição, Universidade Federal de Alagoas GOMES, T. K. C. ; OLIVEIRA, S. L. The role of essential fatty acids on the eicosanoids profi le and its impact on immune response. Nutrire: rev. Soc. Bras. Alim. Nutr. = J. Brazilian Soc. Food Nutr. , São Paulo, SP, v. 35, n. 1, p. 167-186, abr. 2010.
Some considerations on sustainable control over plague of locusts in China

This paper reviews the history of controlling the locust, Locust migratoria manilensis ,in China this century and proposes new assumptions on how to sustainably manage the insect pest.In recent years,biological control of the locust has succeeded to some extent and this strategy had developed in certain areas of our country.In order to prevent or delay development of the locust from solitary phase to gregarious one the biological agents such as Nosema locustae should be used mainly.When high density occurs the IGRs or other chemicals and N.locustae must be used together at certain proportion to reduce the population rapidly,and the N.locustae disease may be epidemic in depressed locust populations in this case.The semiochemicals of locusts should be also studied and developed as one of potential measures for controlling the insect pest.