Miracle-dz/UniFAR-FTUs huggingface dataset:
Anurans from a Cerrado-Atlantic Forest ecotone in Campos Gerais region, southern Brazil

Knowledge of the richness and distribution of anurans living in ecotone regions is still incipient, especially in transition zones between threatened phytogeographic areas like the Cerrado and the Atlantic Forest. This study presents a checklist of anuran amphibians in an ecotone (Cerrado-Atlantic Forest) in the Campos Gerais, Parana State, Brazil. Samplings were conducted in 66 water bodies (ponds) between October 2012 and March 2013. We identified 42 anuran species, six of them in larval stage only and eight of them in adult stage only. The anurofauna accounted for 21.05% of the species registered for the Cerrado and 9.58% of the species found in the Atlantic Forest. Four species are endemic to the Cerrado and eight to the Atlantic Forest. Our results show that this region has a rich anurofauna with species characteristic of different biomes. This study contributes to the process of knowledge production to support further research in ecology, biogeography and conservation of anurans in the Campos Gerais.
On Methods of Interactive NRSFM

Non-rigid Structure From Motion (NRSFM) is highly ill-posed problem due to its inherent objective of 3D non-rigid shape reconstruction from 2D images. Reconstruction of three dimensional single or multi-body deformable structure and estimation of camera poses from two dimensional image streams or monocular video sequences are the main attributes of NRSFM problem. In this report, methods of Interactive NRSFM are being described from series of proposals published in recent years. Interactive and efficient 3D reconstruction of time varying and continuously deformable object, captured in 2D image streams, requires complete and sufficient information of 3D points’ world or camera centric coodinates of objects and camera position simultaneously. Many well posed formulations of NRSFM problem have robustness in 3D reconstruction of deformable shape and camera pose estimation, but computational complexity is high enough. Thus, dense representation of non-rigid structures using large number of shape points cloud does not suit for efficient real time performance. In parallel many methods fail to establish algorithms which do not require prior information or predefined templates of 3D shape in NRSFM problem. Here in this report those potential methods of interactive NRSFM are descriptively elaborated with comparative performance analysis.
LIGHT SCATTERING, FIBER OPTIC- AND CELL-BASED SENSORS FOR SENSITIVE DETECTION OF FOODBORNE PATHOGENS

Rapid and sensitive detection tools are essential in pathogen control and prevention in food and in food processing facilities. The conventional culture methods provide reliable results but the analysis time, labor and the cost associated with these methods often pose a great inconvenience to industrial applications. Biosensor-based detection methods are considered to be promising emerging technologies which are capable of fulfilling the current needs in providing results rapidly with improved sensitivity and specificity. In this review we described three cutting-edge optical sensor technologies: light scattering, fiber optic- and cell-based sensors, which are proven to be useful in pathogen detection from food samples.
Three-dimensional distribution of acid phosphatase-positive thread-like structures "nematolysosomes" in rat pancreatic exocrine cells.

The lysosome is a motile organelle which shows polymorphic structure. Recently, the existence of acid phosphatase-positive thread-like structure has been found in a number of cell types such as macrophages (1, 2, 8, 16, 17), striated muscle cells (11), smooth muscle cells (15) and pinealocytes (9). Although these structure were called "tubular lysosomes" by some investigators, we prefer to use the term of "nematolysosomes" (1) rather than "tubular lysosomes". We have previously reported that the lyososme could transform into nemato-shape, usual spherical-shape and wrapping-shape during heterophagy and autophagy, and the lysosomal transformation was modulated by the cytoskeletal system in macrophages (1, 2). In the exocrine acinar cells, Oliver (12, 13) and Beaudoin et al. (3, 4) found elongated lysosomes which were morphologically similar to nematolysosomes in other cells. The elongated lysosomes were called "basal lysosomes" (12-14) or "snake-like tubules" (3,4). In their previous cytochemical investigations (3, 4, 12-14), it was reported that elongated lysosomes in exocrine cells did not show acid phosphatase (ACPase) activity, although they were positive for trimetaphosphatase (TMPase), aryl sulfatase B, non-specific esterase and nicotinamide adenine dinucleotide phosphate phosphohydrolase (Q-NADPHase). From these cytochemical aspects, the elongated lysosomes in exocrine cells were distinct from other lysosomes. Therefore, Oliver and Yuasa (14) proposed that elongated lysosomes in exocrine acinar cells were an unique population of lysosomes. However, in the present study, we could cytochemically demonstrate acid phosphatase activity of elongated lysosomes in rat pancreatic exocrine acinar cells by employing PIPES buffered fixative. We report here overcoming latency of ACPase activity and the three-dimensional distribution of elongated lysosomes in pancreatic exocrine cells. Adult Wistar rats were perfused with 2% paraformaldehyde and 0.25% glutaraldehyde in 30 mM PIPES buffer, pH 7.4, containing 10% dimethylsulfoxide (DMSO) and 5% sucrose. The pancreas was removed, cut into small blocks and subsequently immersed in the same fixative for 1 hr at 4°C. The tissues were rinsed with 30 mM PIPES buffer, pH 7.4, containing 10% DMSO and 5% sucrose, and then cut into 40-50 im thick sections with a Microslicer (Dosaka EM, Kyoto) or a cryostat. The sections were incubated with the Gomori's ACPase medium (7) for 30 min at room temperature. As a cytochemical control, some of sections were incubated with the reaction medium containing 10 mM sodium fluoride (NaF), an inhibitor of ACPase. TMPase activity as another cytochemical marker for lysosomes was detected by the method of Doty et al. (6). After cytochemical incubation, the sections were rinsed with 30 mM PIPES buffer containing 8% sucrose without DMSO, post-fixed with PIPES buffered 1 % 0s04 for 30 min at 4°C, dehydrated in graded
Optogenetic control of the Bone Morphogenetic Protein signalling pathway through engineered blue light-sensitive receptors

Bone Morphogenetic Proteins (BMPs) are members of the Transforming Growth Factor β (TGFβ) superfamily and have crucial roles during development; including mesodermal patterning and specification of renal, hepatic and skeletal tissues. In vitro developmental models currently rely upon costly and unreliable recombinant BMP proteins that do not enable dynamic or precise perturbation of the BMP signalling pathway. Here, we develop a novel optogenetic BMP signalling system (optoBMP) that enables rapid induction of the canonical BMP signalling pathway through illumination with blue light. We demonstrate the utility of the optoBMP system in multiple human cell lines to initiate signal transduction through phosphorylation and nuclear translocation of SMAD1/5, leading to upregulation of BMP target genes including Inhibitors of DNA binding ID2 and ID4. Furthermore, we demonstrate how the optoBMP system can be used to fine-tune activation of the BMP signalling pathway through variable light stimulation. Optogenetic control of BMP signalling will enable dynamic and high-throughput intervention across a variety of applications in cellular and developmental systems.
Prediction of novel virus–host interactions by integrating clinical symptoms and protein sequences

Motivation: Infectious diseases from novel viruses are becoming a major public health concern. Fast identification of virus–host interactions can reveal mechanistic insights of infectious diseases and shed light on potential treatments and drug discoveries. Current computational prediction methods for novel viruses are based only on protein sequences. Yet, it is not clear to what extent other important features, such as the symptoms caused by the viruses, could contribute to a predictor. Disease phenotypes (i.e., symptoms) are readily accessible from clinical diagnosis and we hypothesize that they may act as a potential proxy and an additional source of information for the underlying molecular interactions between the pathogens and hosts. Results: We developed DeepViral, a deep learning method that predicts potential protein–protein interactions between human and viruses. First, human proteins and viruses were embedded in a shared space using their associated phenotypes, functions, taxonomic classification, as well as formalized background knowledge from biomedical ontologies. By extending a sequence learning model with phenotype features, our model can not only significantly improve over previous sequence-based approaches for inter-species interaction prediction, but also identify pathways of viral targets under a realistic experimental setup for novel viruses. Availability:https://github.com/bio-ontology-research-group/DeepViral Contact: robert.hoehndorf@kaust.edu. sa
Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation

ABC transporters facilitate the movement of a diverse array of molecules across cellular membranes, using power from ATP hydrolysis. While the overall mechanism of the transport cycle has been characterized in detail for several important members of this transporter family, it is less well understood how the activity of ABC transporters is regulated in the cell post-translationally. Here we report the X-ray crystal structure of MlaFB from E. coli, an ABC nucleotide binding domain (MlaF) in complex with its putative regulatory subunit (MlaB). MlaFB constitutes the cytoplasmic portion of the larger MlaFEDB ABC transporter complex, which drives phospholipid transport across the bacterial envelope and is important for maintaining the integrity of the outer membrane barrier. Our data show that the regulatory subunit MlaB, a STAS domain protein, binds to the nucleotide binding domain and is required for its stability. Our structure also implicates a unique C-terminal tail of the ABC subunit, MlaF, in self-dimerization. Both the C-terminal tail of MlaF and the interaction with MlaB are required for the proper assembly of the MlaFEDB complex and its function in cells. This work leads to a new model for how the activity of an important bacterial lipid transporter may be regulated by small binding proteins, and raises the possibility that similar regulatory mechanisms may exist more broadly across the ABC transporter family, from bacteria to humans.
Multiannual infestation patterns of grapevine plant inhabiting Scaphoideus titanus (Hemiptera: Cicadellidae) leafhoppers

Abstract The Nearctic leafhopper Scaphoideus titanus Ball (Hemiptera: Cicadellidae) was accidentally introduced in Europe, where it became the vector of the ‘Candidatus Phytoplasma vitis’ phytoplasma causing the ‘Flavescence dorée’ disease of grapevine plants. A time-varying distributed delay model, simulating the successive occurrences of egg hatching, nymph presence, and adult emergence, is extended here to represent multi-generation infestation patterns of grapevine plants inhabited by eggs, nymphs, and adults. The model extension includes intrinsic mortality, mortality caused by plant dormancy, and low temperatures, development of diapausing and post-diapausing eggs, fecundity rates, and adult longevity. Field observations and published data were used to estimate parameters. The model was validated with five years canopy infestation data from five vineyards not subjected to insecticide treatments and found to have satisfactory explicative and predictive qualities. The model output is most sensitive to a 10% variation in the upper threshold and in the shape parameters of the survivorship function and least sensitive to a 10% variation in the shape parameters of the development function and the survivorship level. Recommendations are made to take into account other factors than temperature and plant phenology and include a wider geographical area in further model development. Résumé La cicadelle néarctique Scaphoideus titanus Ball (Hemiptera: Cicadellidae) a été introduite accidentellement en Europe dans les années ‘50, où elle est devenue le vecteur du « Candidatus Phytoplasma vitis » responsable de la maladie de Flavescence dorée de la vigne. Un modèle de délai distribué dans le temps (time-varying distributed delay model), simulant les évènements successifs des éclosions, de la présence des stades juvéniles et de l’émergence des adultes, a été étendu pour représenter les niveaux d'infestation multi-générationnels de la vigne colonisée par des œufs, des nymphes et des adultes. L'extension du modèle inclut la mortalité intrinsèque, la mortalité causée par la dormance de la plante et les basses températures, le développement des œufs diapausants et post-diapausants, les taux de fécondité et la longévité des adultes. Les observations au champ et les données publiées ont servi de base pour l'estimation des paramètres du modèle. Le modèle a été validé avec les données de cinq années d'infestation de la haie foliaire de cinq vignobles sans traitements insecticides et il a montré des qualités explicatives et prédictives satisfaisantes. Le résultat du modèle est plus sensible à une variation de 10% dans le seuil supérieur et dans les paramètres de forme de la fonction de survie et moins sensible à une variation de 10% dans les paramètres de forme de la fonction de développement et du niveau de survie. Des recommandations sont faites pour prendre en compte d'autres facteurs que la température et la phénologie de la plante et inclure un plus large éventail de zones géographiques pour un développement ultérieur du modèle.
Myomegalin regulates Hedgehog pathway by controlling PDE4D at the centrosome

Mutations in the Hedgehog (Hh) signaling are implicated in birth defects and cancers, including medulloblastoma, one of the most malignant pediatric brain tumors. Current Hh inhibitors face the challenge of drug resistance and tumor relapse, urging new insights in the Hh pathway regulation. Our previous study revealed how PDE4D controls global levels of cAMP in the cytoplasm to positively regulate Hh signaling; in the present study we found that a specific isoform PDE4D3 is tethered to the centrosome by myomegalin, a centrosome/Golgi associated protein. Myomegalin loss dislocates PDE4D3 from the centrosome, leading to local PKA over-activation and inhibition of the Hh signaling, leaving other PKA-related pathways unaffected. Myomegalin loss suppresses the proliferation of granule neuron precursors, and blocks the growth of medulloblastoma in mouse model. Our findings specify a new regulatory mechanism of the Hh pathway, and highlight an exciting therapeutic avenue for Hh-related cancers with reduced side effects.
In vitro Evolution of Antibody Affinity via Insertional Mutagenesis Scanning of an Entire Antibody Variable Region

We report the first systematic combinatorial exploration of affinity enhancement of antibodies by insertions and deletions (InDels). Transposon-based introduction of InDels via the method TRIAD was used to generate large libraries with random in-frame InDels across the entire scFv gene that were further recombined and screened by ribosome display. Knowledge of potential insertion points from TRIAD libraries formed the basis of exploration of length and sequence diversity of novel insertions by insertional-scanning mutagenesis (ISM). An overall 256-fold affinity improvement of an anti-IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutations validates this approach and suggests that the results of this InDel approach and conventional exploration of point mutations can synergize to generate antibodies with higher affinity. Significance Insertion/deletion (InDel) mutations play key roles in genome and protein evolution. Despite their prominence in evolutionary history, the potential of InDels for changing function in protein engineering by directed evolution remains unexplored. Instead point mutagenesis is widely used. Here we create antibody libraries containing InDels and demonstrate that affinity maturation can be achieved in this way, establishing an alternative to the point mutation strategies employed in all previous in vitro selections. These InDels mirror the observation of considerable length variation in loops of natural antibodies originating from the same germline genes and be combined with point mutations, making both natural sources of functional innovation available for artificial evolution in the test tube.
Neuroendocrine mechanisms governing sex-differences in chronic pain involve prolactin receptor sensory neuron signaling

Many clinical and preclinical studies report higher prevalence and severity of chronic pain in females. We used hyperalgesic priming with interleukin 6 (IL-6) priming and PGE2 as a second stimulus as a model for pain chronicity. Intraplantar IL-6 induced hypersensitivity was similar in magnitude and duration in both males and females, while both paw and intrathecal PGE2 hypersensitivity was more persistent in females. This difference in PGE2 response was dependent on both circulating estrogen and translation regulation signaling in the spinal cord. In males, the duration of hypersensitivity was regulated by testosterone. Since the prolactin receptor (Prlr) is regulated by reproductive hormones and is female-selectively activated in sensory neurons, we evaluated whether Prlr signaling contributes to hyperalgesic priming. Using ΔPRL, a competitive Prlr antagonist, and a mouse line with ablated Prlr in the Nav1.8 sensory neuronal population, we show that Prlr in sensory neurons is necessary for the development of hyperalgesic priming in female but not male mice. Overall, sex-specific mechanisms in the initiation and maintenance of chronic pain are regulated by the neuroendocrine system and, specifically, sensory neuronal Prlr signaling. Significance Statement Females are more likely to experience chronic pain than males, but the mechanisms that underlie this sex difference are not completely understood. Here, we demonstrate that the duration of mechanical hypersensitivity is dependent on circulating sex hormones in mice – where estrogen caused an extension of sensitivity and testosterone was responsible for a decrease in the duration of the hyperalgesic priming model of chronic pain. Additionally, we demonstrated that Prolactin receptor expression in Nav1.8+ neurons was necessary for hyperalgesic priming in female, but not male mice. Our work demonstrates a female-specific mechanism for the promotion of chronic pain involving the neuroendrocrine system and mediated by sensory neuronal prolactin receptor.
Pooled CRISPR screening at high sensitivity with an empirically designed sgRNA library

Given their broad utility in functionally annotating genomes, the experimental design of genome-scale CRISPR screens can vary greatly and criteria for optimal experimental implementation and library composition are still emerging. In this study, we report advantages of conducting viability screens in selected Cas9 single cell clones in contrast to Cas9 bulk populations. We further systematically analyzed published CRISPR screens in human cells to identify single-guide (sg)RNAs with consistent high on-target and low off-target activity. Selected guides were collected in a new genome-scale sgRNA library, which efficiently identifies core and context-dependent essential genes. In summary, we show how empirically designed libraries in combination with an optimised experimental design increase the dynamic range in gene essentiality screens at reduced library coverage.
CD13 is a Critical Regulator of Cell-cell Fusion in Osteoclastogenesis

In vertebrates, bone formation is dynamically controlled by the activity of two specialized cell types: the bone-generating osteoblasts and bone-degrading osteoclasts. Osteoblasts produce the soluble receptor activator of NFκB ligand (RANKL) that binds to its receptor RANK on the surface of osteoclast precursor cells to promote osteoclastogenesis, a process that involves cell-cell fusion and assembly of molecular machinery to ultimately degrade the bone. CD13 is a transmembrane aminopeptidase that is highly expressed in cells of myeloid lineage has been shown to regulate dynamin-dependent receptor endocytosis and recycling and is a necessary component of actin cytoskeletal organization. In the present study, we show that CD13-deficient mice display a normal distribution of osteoclast progenitor populations in the bone marrow, but present a low bone density phenotype. Further, the endosteal bone formation rate is similar between genotypes, indicating a defect in osteoclast-specific function in vivo. Loss of CD13 led to exaggerated in vitro osteoclastogenesis as indicated by significantly enhanced fusion of bone marrow-derived multinucleated osteoclasts in the presence of M-CSF and RANKL, resulting in abnormally large cells with remarkably high numbers of nuclei with a concomitant increase in bone resorption activity. Similarly, we also observed increased formation of multinucleated giant cells (MGC) in CD13KO bone marrow progenitor cells stimulated with IL-4 and IL-13, suggesting that CD13 may regulate cell-cell fusion events via a common pathway, independent of RANKL signaling. Mechanistically, while expression levels of the fusion-regulatory proteins dynamin and DC-STAMP are normally downregulated as fusion progresses in fusion-competent mononucleated progenitor cells, in the absence of CD13 they are uniformly sustained at high levels, even in mature multi-nucleated osteoclasts. Taken together, we conclude that CD13 may regulate cell-cell fusion by controlling expression and localization of key fusion proteins that are critical for both osteoclast and MGC fusion.
Movement pattern and home range of Roman Chrysoblephus laticeps

The movement behaviour of adult Roman Chrysoblephus laticeps (Sparidae) was investigated using mark-and-recapture techniques in the Goukamma Marine Protected Area (GMPA) and the Tsitsikamma National Park (TNP) on the South African temperate south coast. The study was designed to improve the spatial resolution of previous studies on Roman that suggested residence behaviour, but which could not estimate home range size. A combination of conventional barbed dart tags and visible implant fluorescent elastomer (VIFE) tags were used to tag Roman from a skiboat in the GMPA. Roman were tagged with dart tags from the shore in the TNP. Of the recaptures, 61% were within 50m of the tagging position, confirming that Roman are very resident. A few fish, independent of size and sex, moved distances up to 4km. A model was developed to quantify the degree of residence, by accounting for tag loss, mortality and the distribution of recovery effort. The probability of a Roman remaining within an area of 1ha is 0.91 (GMPA) and 0.94 (TNP) — such a small home range suggesting that individual Roman would benefit from small MPAs.