Miracle-dz/UniFAR-FTUs huggingface dataset:
A new specimen with skull and vertebrae of Najash rionegrina (Lepidosauria: Ophidia) from the early Late Cretaceous of Patagonia

The limbed snake Najash rionegrina from the Cenomanian (early Late Cretaceous) of the La Buitrera Palaeontological Area (LBPA), northern Patagonia is a key taxon in any study of the origin and early evolution of snakes. The original concept of the taxon was based on the holotype and a number of referred specimens including an isolated partial skull; a conservative rebuttal argued this concept was too broad due to the lack of association between the holotype elements and the referred specimens. Here we describe a new snake specimen consisting of a partial skull and closely associated vertebrae from the La Buitrera Locality, one of many productive snake localities within the LBPA. The analysis of the vertebrae of the new specimen identifies distinct features shared with the vertebrae of the N. rionegrina holotype; the partial skull of the new specimen is also identical to the partial skull that formed part of the original concept of N. rionegrina. Phylogenetic analysis, using data from the type and referred specimens, and new materials described here, reconstructs N. rionegrina as a basal snake in a ‘madtsoiid’ clade outside of crown-group Serpentes. These new morphologies, and autapomorphies recognized in character analyses, permit the construction of a new and expanded diagnosis of N. rionegrina.
An in-Silico Approach to Understanding the Structure-Function: A Molecular Dynamics Simulation Study of Rand Serine Protease Properties from Bacillus Subtilis in Aqueous Solvents

Serine proteases from the Bacillus species extensively applied in the biotechnological application [1,2] such as detergent, leather and food industries, frequently under non-physiological conditions. New proteases with improved performance at extreme temperatures and in the presence of chemical additives may have great economic potential. The increasing availability of genetic sequences from completely different environments makes homology-based screening an attractive strategy for the discovery of new proteases [3]. So far, the broad investigation on proteases gave the basic understanding of their catalytic mechanism and their structure-function. Computational structure analysis and homology modeling can be a key process for the 3D structure reconstruction which facilitates the protein-protein interaction research. Protein crystal is the basic necessity to obtain the 3D structure [4].
Multilevel Analysis for Repeated Measures Data in Lambs1

The study was conducted to compare the individual growth curves models and to detect individual differences in the growth rate by a performing multilevel analysis. The data set used for this purpose consisted of live weight records of 52 crossbred lambs from birth to 182 days of age. There were 670 observations in level-1 units which were the repeated measurements over time, and there were 52 observations in level-2 units which were lambs. In the study, parameter estimation of timeindependent covariate factors, such as gender, birth type and birth weight, was performed by using five different models within the framework of multilevel modeling. LRT, AIC and BIC were used for the selection of the best model. The “Conditional Quadratic Growth Model-B” provided the best fit to the data set. The multilevel analysis indicated that linear and quadratic growth in lambs was significant. According to the results of the study, individual growth curves can be investigated using multilevel modeling in animal studies which is an important parameter of the individual growth rate.
An improved control efficacy against tobacco bacterial wilt by an engineered Pseudomonas mosselii expressing the ripAA gene from phytopathogenic Ralstonia solanacearum

The environmental bacterium Pseudomonas mosselii produces antagonistic secondary metabolites with inhibitory effects on multiple plant pathogens, including Ralstonia solanacearum, the causal agent of bacterial wilt. In this study, an engineered P. mosselii strain was generated to express R. solanacearum ripAA, which determines incompatible interactions with tobacco plants. The ripAA gene together with its native promoter was integrated into the P. mosselii chromosome. The resulting strain showed no difference in antimicrobial activity against R. solanacearum. Promoter-LacZ fusion and RT-PCR experiments demonstrated that the ripAA gene was transcribed in culture media. Compared with that of the wild type, the engineered strain reduced the disease index by 9.1% for bacterial wilt on tobacco plants. A transcriptome analysis was performed to identify differentially expressed genes in tobacco plants, and the results revealed that ethylene-and jasmonate-dependent defense signaling pathways were induced. These data demonstrated that the engineered P. mosselii expressing ripAA enables improved biological control against tobacco bacterial wilt by the activation of host defense responses. Importance Nowadays, the use of biocontrol agents is more and more popular in agriculture, but they cannot replaced of chemical agents mostly, due to the poorer control effect. So the study about how to improve the efficacy of biocontrol agents become necessary and urgent. We increase the efficacy against plant pathogen through introducing an avirulence gene from plant pathogen into the biocontrol agent based on “gene to gene” hypothesis. The new engineered strain can improve the systemic resistance and elicit primary immune response of plants. Our research not only provides a new strategy for genetic modification of biocontrol agent, a number of avirulence gene from pathogen or plant can be tested to be expressed in different biocontrol agents to antagonize plant disease, but also help the study of interaction between phythopathogenic avirulence gene and host.
Multi-omics analysis of AML cells treated with azacitidine reveals highly variable cell surface proteome remodeling

Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor (DNMTi) widely used to treat MDS and AML, yet the impact of AZA on the cell surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines (KG1a, HL60, HNT34, and AML193), representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome (methylation array), the transcriptome (gene expression array), and the cell surface proteome (glycoprotein capture with SILAC labeling). Untreated AML cell lines showed substantial overlap in their methylomes, transcriptomes, and cell surface proteomes. AZA treatment globally reduced DNA methylation in all cell lines, but changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly up-regulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteomics analysis found no commonly regulated proteins. Gene Set Enrichment Analysis (GSEA) of differentially-regulated RNA and surface proteins showed a decrease in metabolism pathways and an increase in immune defense response pathways. As such, AZA treatment in four AML cell lines had diverse effects at the individual gene and protein level, but converged to regulation of metabolism and immune response at the pathway level. Given the heterogeneous response of AZA in the four cell lines at the gene and protein level, we discuss potential therapeutic strategies for combinations with AZA.
Size-structured habitat selection by arapaima in floodplain lakes of the Lower Amazon

Human modification of floodplain ecosystems is widespread and a major threat to fish populations, particularly in the tropics where fish diversity and rates of floodplain degradation are high. Identifying measures to minimize the susceptibility of floodplain fishes to habitat modification requires understanding dry‐season lake habitat selection for species of conservation concern. This study examined the effects of environmental factors on dry‐season floodplain lake habitat selection by arapaima (Arapaima spp.) and determined the extent to which they differed across three size classes. In floodplain lakes of the lower Amazon River, variables were measured at locations representing habitat availability and compared with measurements taken where arapaima were observed during surface breathing. Regression models were used to account for between‐lake variation in the presence of arapaima owing to nearby fishing communities. The probability of arapaima presence at each sample location was modelled based on the variables measured. The results indicated that arapaima expressed distinct habitat selection patterns, which differed significantly across size classes. The general pattern observed was that all arapaima were more likely to be found in deeper, more turbid, and higher conductivity locations, whereas smaller arapaima were more likely to remain near dense beds of floating macrophytes. The probability of arapaima presence differed among fishing community territories, reflecting differences in management schemes. Deeper, macrophyte‐rich sections of floodplain lakes appear to provide key habitats for arapaima and deserve consideration for becoming priority targets for conservation of the rich diversity of fish species in these systems.
Complete mitochondrial genome of the four-lined snake, Elaphe quatuorlineata (Bonnaterre, 1790)

Abstract Here, we present complete mitochondrial genome of the four-lined snake, Elaphe quatuorlineata (Bonnaterre, 1790) and its comparison with closely related E. sauromates (Pallas, 1814). The complete sequence of the mitogenome is 17,183 bp long and consists of 13 protein-coding genes, two rRNA and 22 tRNA genes, and two control regions. It possesses the same gene order as other mitogenomes of Elaphe spp. and the base composition is as follows: 35.0% (A), 26.7% (C), 25.6% (T), and 12.7% (G), with an A + T bias (60.6%). The presented mitogenome will provide new data for phylogenetic analysis within phylogenetically close western Palearctic species of the genus Elaphe.
Programmable patterns in a DNA-based reaction-diffusion system

Biology offers compelling proof that macroscopic “living materials” can emerge from reactions between diffusing biomolecules. Here, we show that molecular self-organization could be a similarly powerful approach for engineering functional synthetic materials. We introduce a programmable DNA-hydrogel that produces tunable patterns at the centimeter length scale. We generate these patterns by implementing chemical reaction networks through synthetic DNA complexes, embedding the complexes in hydrogel, and triggering with locally applied input DNA strands. We first demonstrate ring pattern formation around a circular input cavity and show that the ring width and intensity can be predictably tuned. Then, we create patterns of increasing complexity, including concentric rings and non-isotropic patterns. Finally, we show “destructive” and “constructive” interference patterns, by combining several ring-forming modules in the gel and triggering them from multiple sources. We further show that computer simulations based on the reaction-diffusion model can predict and inform the programming of target patterns.
Structural basis of the differential binding of engineered knottins to integrins αVβ3 and α5β1

Targeting both integrins αVβ3 and α5β1 simultaneously appears to be more effective in cancer therapy than targeting each one alone. The structural requirements for bispecific binding of ligand to integrins has not been fully elucidated. RGD-containing knottin 2.5F binds selectively to αVβ3 and α5β1, whereas knottin 2.5D is αVβ3-specific. To elucidate the structural basis of this selectivity, we determined the structures of 2.5F and 2.5D as apo-proteins and in complex with αVβ3, and compared their interactions with integrins using molecular dynamics simulations. These studies show that 2.5D engages αVβ3 by an induced fit, but conformational selection of a flexible RGD loop accounts for high affinity selective binding of 2.5F to both integrins. The contrasting binding of the highly flexible low affinity linear RGD peptides to multiple integrins, suggests that a “Goldilocks zone” of conformational flexibility of the RGD loop in 2.5F underlies its selective binding promiscuity to integrins.
A multi-modal proteomics strategy for characterizing posttranslational modifications of tumor suppressor p53 reveals many sites but few modified forms

Post-translational modifications (PTMs) are found on most proteins, particularly on “hub” proteins like the tumor suppressor p53, which has over 100 possible PTM sites. Substantial crosstalk between PTM sites underlies the ability of such proteins to integrate diverse signals and coordinate downstream responses. However, disentangling the combinatorial explosion in global PTM patterns across an entire protein (“modforms”) has been challenging, as conventional peptide-based mass spectrometry strategies (so-called “bottom-up” MS) destroy such global correlations. Alternatively, direct analysis of intact and modified proteins using “top-down” MS retains global information. Here, we applied both strategies to recombinant p53 phosphorylated in vitro with Chk1 kinase, which exhibited 41 modified sites by bottom-up MS, but no more than 8 modified sites per molecule detected by top-down MS. This observation that many low-abundance modifications comprise relatively few modforms above a 1% threshold indicates that endogenous p53 PTM complexity may be more definable than previously thought.
Campylobacter Phage Isolation and Characterization: What We Have Learned So Far

Lytic Campylobacter phages, which can be used to combat this pathogen in animals and on food products, have been studied for more than 30 years. Though, due to some peculiarities of the phages, which hampered their isolation and particularly their molecular analysis for a long time, progress in this research field was rather slow. Meanwhile, the situation has changed and much more is known about the biology and genetics of those phages. In this article, we address specific issues that should be considered when Campylobacter phages are studied, starting with the isolation and propagation of the phages and ending with a thorough characterization including whole-genome sequencing. The basis for advice and recommendations given here is a careful review of the scientific literature and experiences that we have had ourselves with Campylobacter phages.
Bear Response to Supplemental Feed Offered to Reduce Tree Peeling

: Black bears ( Ursus americanus ) strip bark from coniferous trees to feed on newly forming vascular tissue during spring. Damage inflicted through this behavior can be extremely detrimental to the health and economic value of timber stands. A supplemental feeding program to provide bears an alternative food source during spring is practiced by some resource managers. We evaluated the efficacy of the program and conducted concurrent studies to assess select behavioral characteristics of feeding bears and impacts of providing supplemental feed on nutritional status of bears. The efficacy study revealed the percentage of damaged trees in stands with foraging bears varied from 2% to 52%. When supplemental feeding was introduced on these stands, damage was reduced to approximately 10% of that sustained on untreated stands. Concurrent experiments provided insightful data on bear use of feeding stations. Numerous bears fed at the stations, including females with and without cubs, yearlings, and boars. Bear feeding bouts at the stations were generally short, less than 30 minutes. Bears generally fed alone, although 2 to 3 adult bears were observed at a feeder simultaneously and the feeding partners were not consistent. There was little antagonistic behavior observed around the feeders, and no evidence that this behavior inhibited foraging opportunities for long. On the rare occasion a bear was driven from a feeder it returned later that same day to feed, generally within an hour. Supplemental feeding also did not affect the home range sizes of bears in feeding areas, but it may serve to concentrate bears in a particular location. Bears consuming supplemental feed did gain a significant nutritional advantage while feeding, but this did not equate to long term increases in age-specific body masses or fat content.
Evaluation of colorectal cancer subtypes and cell lines using deep learning

A deep learning approach refines the state-of-the-art subtypes of colorectal cancer and evaluates the fidelity of cell lines that model cancer. Colorectal cancer (CRC) is a common cancer with a high mortality rate and a rising incidence rate in the developed world. Molecular profiling techniques have been used to better understand the variability between tumors and disease models such as cell lines. To maximize the translatability and clinical relevance of in vitro studies, the selection of optimal cancer models is imperative. We have developed a deep learning–based method to measure the similarity between CRC tumors and disease models such as cancer cell lines. Our method efficiently leverages multiomics data sets containing copy number alterations, gene expression, and point mutations and learns latent factors that describe data in lower dimensions. These latent factors represent the patterns that are clinically relevant and explain the variability of molecular profiles across tumors and cell lines. Using these, we propose refined CRC subtypes and provide best-matching cell lines to different subtypes. These findings are relevant to patient stratification and selection of cell lines for early-stage drug discovery pipelines, biomarker discovery, and target identification.
Simultaneous, non-invasive measurements of skin blood flow and oxygenation in healthy humans

Adequate blood flow within microcirculation and sufficient tissue oxygenation are essential for tissue health. However, the quantitative understanding of dynamics between the microvascular blood flow and oxygenation remains limited. The aim of this study was to explore and interpret simultaneous measurements of skin blood flux (BF) and oxygenation parameters (OXY) recorded from healthy skin. Measurements were recorded using a recently developed (Moor Instruments Ltd, UK) combined Laser Doppler Flowmetry (LDF) and White Light Spectroscopy (WLS) technique, which offer an easy to perform assessment of skin microcirculation and skin oxygenation. In this thesis, two open studies have been conducted in cohorts of healthy volunteers to evaluate combined LDF-WLS measurements and to study the relationship between skin BF and OXY. The engineering challenge of this thesis was to apply signal processing methods to analyse BF and OXY parameters and to extract information that reflect the physiological characteristics of the tissue. Signal processing methods such filtering, convolution, Fourier transform and others served as tools to identify different properties of the signals and subsequently describe the biological systems. The measurements acquired across wide range of values led to mathematical description of the relationship between skin BF and oxygenation and revealed different oscillatory characteristics in BF and OXY signals. The analysis showed resting BF and OXY signals have the highest coherence across low frequency bands. Furthermore, OXY signals are delayed in respect to BF signals. Signal obtained during thermally induced vasodilation showed a shift in signal power to the cardiac frequency band. In conclusion, simultaneous measurements of skin BF and OXY signals in combination with signal processing techniques offer an extended assessment of microvascular function, which may complement clinical assessment of tissue status. Further work is now required to combine presented in this thesis BF and OXY characteristics with other available analysis into clinically useful assessment.
Zn2+ Intoxication of Mycobacterium marinum during Dictyostelium discoideum Infection Is Counteracted by Induction of the Pathogen Zn2+ Exporter CtpC

Microelements are essential for the function of the innate immune system. A deficiency in zinc or copper results in an increased susceptibility to bacterial infections. ABSTRACT Macrophages use diverse strategies to restrict intracellular pathogens, including either depriving the bacteria of (micro)nutrients such as transition metals or intoxicating them via metal accumulation. Little is known about the chemical warfare between Mycobacterium marinum, a close relative of Mycobacterium tuberculosis (Mtb), and its hosts. We use the professional phagocyte Dictyostelium discoideum to investigate the role of Zn2+ during M. marinum infection. We show that M. marinum senses toxic levels of Zn2+ and responds by upregulating one of its isoforms of the Zn2+ efflux transporter CtpC. Deletion of ctpC (MMAR_1271) leads to growth inhibition in broth supplemented with Zn2+ as well as reduced intracellular growth. Both phenotypes were fully rescued by constitutive ectopic expression of the Mtb CtpC orthologue demonstrating that MMAR_1271 is the functional CtpC Zn2+ efflux transporter in M. marinum. Infection leads to the accumulation of Zn2+ inside the Mycobacterium-containing vacuole (MCV), achieved by the induction and recruitment of the D. discoideum Zn2+ efflux pumps ZntA and ZntB. In cells lacking ZntA, there is further attenuation of M. marinum growth, presumably due to a compensatory efflux of Zn2+ into the MCV, carried out by ZntB, the main Zn2+ transporter in endosomes and phagosomes. Counterintuitively, bacterial growth is also impaired in zntB KO cells, in which MCVs appear to accumulate less Zn2+ than in wild-type cells, suggesting restriction by other Zn2+-mediated mechanisms. Absence of CtpC further epistatically attenuates the intracellular proliferation of M. marinum in zntA and zntB KO cells, confirming that mycobacteria face noxious levels of Zn2+. IMPORTANCE Microelements are essential for the function of the innate immune system. A deficiency in zinc or copper results in an increased susceptibility to bacterial infections. Zn2+ serves as an important catalytic and structural cofactor for a variety of enzymes including transcription factors and enzymes involved in cell signaling. But Zn2+ is toxic at high concentrations and represents a cell-autonomous immunity strategy that ensures killing of intracellular bacteria in a process called zinc poisoning. The cytosolic and lumenal Zn2+ concentrations result from the balance of import into the cytosol via ZIP influx transporters and efflux via ZnT transporters. Here, we show that Zn2+ poisoning is involved in restricting Mycobacterium marinum infections. Our study extends observations during Mycobacterium tuberculosis infection and explores for the first time how the interplay of ZnT transporters affects mycobacterial infection by impacting Zn2+ homeostasis.