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We have imaged the particles of Brazilian soils at multiple length scales, from a few microns to millimeters, and soil particle size distributions were calculated with unmatched precision. The analysis included the Amazonian soil “Terra Mulata de Índio” (TMI), an anthropogenic soil (Anthrosol) with sustained fertility and a large amount of stabilized organic matter. Firstly, the soils were imaged ex situ, without any chemical processing, with sequential electron scanning of the pelletized soil samples, covering a total area of 8 × 8 mm. Secondly, it was performed a computational analysis of the large-field X-ray images assembled from hundreds of adjacent elemental maps, thus resulting in high-definition images (4800 × 4800 pixels). This analytical approach provides a large sampling with the identification of > 10,000 particles over the scanned area. The particles identified consisted of Al, C, Ca, Cr, F, Fe, Mg, Mn, Na, O, P, S, Si and Ti. A significantly larger concentration of C-, Ca- and P-based particles, of up to 100 μm 2 of cross-section area, was found in TMI samples in comparison with oxisol and ultisol soils. While the mean distance between neighboring C, Ca and P particles in TMI was of 40–70 μm, the value was of hundreds of microns in oxisol and ultisol. Furthermore, mapping of micrometric carbon particles by Raman spectroscopy indicated that they have a graphitic structure with a large amount of defects, partially associated with particle oxidation, although a well-preserved sp 2 graphitic structure is also present. From a technological perspective, improved soil amendments, such as biochar, can be rationally designed from the “fingerprint” described here for soil particles of Amazonian Anthrosols (i.e., morphological and structural characteristics), which can result in an increase in fertility and the optimization of carbon sequestration in the future. [ABSTRACT FROM AUTHOR]

• Ag-TiNT is effective against Gram-positive bacteria and Gram-negative bacteria. • XRD pattern demonstrated a different morphology compared with other nanotubes. • The tubular morphology was lost after the addition of silver ions, changing to nanosheets. • This is related to a higher interlayer concentration of silver, generating the change from nanotubes to nanosheets. Titanium nanostructures have been widely studied due to their potential for various applications. One of its most promising applications is in the antibacterial activity, in particular, of Silver Titanate Nanoubes (Ag-TiNT). The determining factors for the high efficiency process against bacteria are related to the surface area of the material and the main metal that composes it. Microbial infections continue to be one of the most serious complications in different areas, particularly in the hospital environment. This work was investigated as bactericidal properties of Silver Titanate nanotubes against Gram-negative bacteria of Escherichia coli and Pseudomonas aeruginosa and Gram-positive bacteria of Staphylococcus aureus , in systems containing only the Ag-TiNT for the antibiotic compounds. In addition, the study of the main, vibrational and morphological characteristics of Ag-TiNT was carried out. As a result, as microdilution plates accompanying only the positive anti-bacterial dish, while in the microdilution plates containing Ag-TiNT with antibiotics, divergent results. Abstract: Ag-TiNT morphology structures, electron microscopy (SEM, TEM), Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR) and dispersion spectroscopy were detected of X-ray energy (EDS). [Display omitted] [ABSTRACT FROM AUTHOR]

Titanium nanotubes have attractive morphological and physicochemical properties for several applications, such as high surface area, mesoporous structure, good stability, ion exchange capacity, and antibacterial property. Therefore, the field of nanotube applications is increasingly expanding, such as in solar cells sensitized by dye, photocatalysis, and antibacterial activity, among others. Therefore, a study of the antibacterial properties of sodium titanate nanotubes (Na-TiNTs) was carried out together with physicochemical characterizations, such as Raman spectroscopy which shows a peak characteristic of Na-O-Ti from nanotube-agglomerated regions. The XRD diffractogram confirmed the Raman spectra and evidenced the crystalline structure associated to Na-TiNT, which showed the characteristic peaks of the sodium trititanate crystal. SEM and TEM images showed the morphology of hollow nanotubes and forming semispherical particles. EDS shows the percentage values of each of the compounds in the Na-TiNT. The bacterial activity of the Na-TiNT was analyzed in Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. Na-TiNT modified the activity of the gentamicin and norfloxacin antibiotics against multiresistant strains. Synergistic effects against Gram-positive S. aureus 10 and Gram-negative P. aeruginosa 15 bacteria were observed when the Na-TiNT was associated with gentamicin, reducing the concentration of this antibiotic that is required to inhibit bacterial growth. Another synergic effect was observed for S. aureus 10 with norfloxacin. [ABSTRACT FROM AUTHOR]

Titanium nanotubes have attractive morphological and physicochemical properties for several applications, such as high surface area, mesoporous structure, good stability, ion exchange capacity, and antibacterial property. Therefore, the field of nanotube applications is increasingly expanding, such as in solar cells sensitized by dye, photocatalysis, and antibacterial activity, among others. Therefore, a study of the antibacterial properties of sodium titanate nanotubes (Na-TiNTs) was carried out together with physicochemical characterizations, such as Raman spectroscopy which shows a peak characteristic of Na-O-Ti from nanotube-agglomerated regions. The XRD diffractogram confirmed the Raman spectra and evidenced the crystalline structure associated to Na-TiNT, which showed the characteristic peaks of the sodium trititanate crystal. SEM and TEM images showed the morphology of hollow nanotubes and forming semispherical particles. EDS shows the percentage values of each of the compounds in the Na-TiNT. The bacterial activity of the Na-TiNT was analyzed in Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa. Na-TiNT modified the activity of the gentamicin and norfloxacin antibiotics against multiresistant strains. Synergistic effects against Gram-positive S. aureus 10 and Gram-negative P. aeruginosa 15 bacteria were observed when the Na-TiNT was associated with gentamicin, reducing the concentration of this antibiotic that is required to inhibit bacterial growth. Another synergic effect was observed for S. aureus 10 with norfloxacin. [ABSTRACT FROM AUTHOR]

As consequence of the various genomic sequencing projects, an increasing volume of biological sequence data is being produced. Although machine learning algorithms have been successfully applied to a large number of genomic sequence-related problems, the results are largely affected by the type and number of features extracted. This effect has motivated new algorithms and pipeline proposals, mainly involving feature extraction problems, in which extracting significant discriminatory information from a biological set is challenging. Considering this, our work proposes a new study of feature extraction approaches based on mathematical features (numerical mapping with Fourier, entropy and complex networks). As a case study, we analyze long non-coding RNA sequences. Moreover, we separated this work into three studies. First, we assessed our proposal with the most addressed problem in our review, e.g. lncRNA and mRNA; second, we also validate the mathematical features in different classification problems, to predict the class of lncRNA, e.g. circular RNAs sequences; third, we analyze its robustness in scenarios with imbalanced data. The experimental results demonstrated three main contributions: first, an in-depth study of several mathematical features; second, a new feature extraction pipeline; and third, its high performance and robustness for distinct RNA sequence classification. Availability: https://github.com/Bonidia/FeatureExtraction_BiologicalSequences [ABSTRACT FROM AUTHOR]

Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity. [ABSTRACT FROM AUTHOR]

Background: Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste. Results: The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication. Conclusions: The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators. [ABSTRACT FROM AUTHOR]

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots. [ABSTRACT FROM AUTHOR]

The unique electronic and vibrational properties of linear carbon chains (LCCs) have attracted close attention from the scientific community in recent years. Raman spectroscopy addressing the LCC spectral signature around 1850 cm−1 has been widely used to identify the LCC and probe electronic and vibrational properties as a function of carbon length. Despite the number of works available in literature, some aspects of the LCC's aforementioned properties remain unclear. Using a combination of confocal and Tip-enhanced Raman Spectroscopy (TERS), along with different laser lines, this work addresses important aspects of the optical resonance window of LCCs encapsulated by multi-walled carbon nanotubes (MWCNTs) (i.e. LCC@MWCNT) as well as an elusive Raman signature around 1637 cm−1, which is assigned to the LCC's longitudinal acoustic (LA) phonon mode at the X point (zone edge), which becomes Raman active likely due to disorder effects. First-principles calculations endorse our conclusions. [Display omitted] [ABSTRACT FROM AUTHOR]

This study utilized the confocal Raman microspectroscopy ( CRM) technique for the first time to investigate the degree of the penetration of toluidine blue-orto ( TBO) in artificial caries lesions produced by two distinct caries-inducing models. The dentin specimens ( n = 10) were divided into three groups: control, in vitro and in situ. Thereafter, the lesion depth and the demineralization level were evaluated by cross-sectional microhardness ( CSMH). CRM mapping across the dentin surface was assessed after the dye application. The CSMH and CRM data were analyzed by t-test and ANOVA, respectively ( P < 0.05). The values of the lesion depth and the demineralization areas were higher for in situ samples ( P < 0.05). The TBO penetration values (μm) for the control, in vitro and in situ groups were 44.8 ± 5.6, 46.1 ± 4.5 and 51.2 ± 8.5, respectively. There were no statistically significant differences among the groups ( P > 0.05). The rate of TBO penetration was detected up to about <50 μm and the demineralization level did not influence the results. These results have showed promising parameters to develop new protocols for deep caries lesions management using photodynamic antimicrobial chemotherapy. [ABSTRACT FROM AUTHOR]

Linear carbon chains (LCCs) are one-dimensional materials with unique properties, including high Debye temperatures and restricted selection rules for phonon interactions. Consequently, their Raman C-band frequency's temperature dependence is a probe to their thermal properties, which are well described within the Debye formalism even at room temperatures. Therefore, with the basis on a semiempirical approach we show how to use the C band to evaluate the LCCs' internal energy, heat capacity, coefficient of thermal expansion, thermal strain, and Grüneisen parameter, providing universal relations for these quantities in terms of the number of carbons atoms and the temperature. [ABSTRACT FROM AUTHOR]

The hydroxyapatite of fossil bones can provide paleoenvironmental information, because throughout the fossil-diagenetic process, the fossils can incorporate elements from the sedimentary rocks that involved them. In this way, the present study aimed for geochemical patterns in mesosaurid bones and their respective host rocks to project the paleoenvironmental conditions at deposition/diagenesis' time. For this purpose, Raman Spectroscopy and X-Ray Fluorescence analysis were performed. The samples came from Irati ( S 1 – São Matues do Sul, S 2 – Assistência, S 4 – Aceguá e S 5 – São Gabriel) and Mangrullo ( S 3 – Uruguay) Formations. We found similar geochemical composition between S 1 and S 5 ; S 3 and S 4 which also indicates a similar paleoenvironmental context. The samples S 1 and S 5 have relatively high Al, Si and Sr contents which can represent acidic conditions and high depths. The second set (S 3 and S 4) have similar contents of Al, Si and Ca, but it is worth to note that the Si and Ca contents are slightly different. The Si and Ca contents suggest that S 3 was slightly deeper and less acidic when compared to S 4. In general, the first set (S 1 and S 5) were deeper and more acidic than the second (S 3 and S 4). The S 2 sample is out of line with the others, corresponding to shallow or coastal and more basic paleoenvironment. Overall, our results agree with previous studies about the past environment where mesosaurs lived. Also, shows that spectroscopy techniques are reliable and should be used to refine paleoenvironmental interpretations. [ABSTRACT FROM AUTHOR]

Silver nanoparticles (AgNPs) have a large number of technological applications, such as photonic devices, molecular diagnostics, antimicrobial coating and biomedical devices. These nanomaterials can be synthesized using common fungi, which represents a green approach with the additional advantage of biocompatibility. Here we applied Tip-Enhanced Raman Spectroscopy (TERS) to obtain optical characterization with resolution beyond the diffraction limit of AgNPs produced by Rhodotorula glutinis and Rhodotorula mucilaginosa fungi. Those fungi are conventional found in ordinary soil of north part of Brazil, which biosynthesize core-shell AgNPs with protein-capping layer. With TERS we were able to investigate with lateral resolution of few nanometers the size and structure of the protein capping layer, how it interacts with the Ag core, and how sensitive the system (core + protein) is to visible light illumination. Despite the complex data generated which depends on the orientation of the protein, which is highly, it was possible to detect the stretching of the S - S sulfur bridge in amino acids. This stretch band is induced by a trans C α - S conformation acid on Rm-AgNPs, thus showing the potential of characterization of TERS in nanobiosystems. [ABSTRACT FROM AUTHOR]