inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction

Rescoring of mass spectrometry (MS) search results using spectral predictors can strongly increase peptide spectrum match (PSM) identification rates. This approach is particularly effective when aiming to search MS data against large databases, for example, when dealing with nonspecific cleavage in immunopeptidomics or inflation of the reference database for noncanonical peptide identification. Here, we present inSPIRE (in silico Spectral Predictor Informed REscoring), a flexible and performant open-source rescoring pipeline built on Prosit MS spectral prediction, which is compatible with common database search engines. inSPIRE allows large-scale rescoring with data from multiple MS search files, increases sensitivity to minor differences in amino acid residue position, and can be applied to various MS sample types, including tryptic proteome digestions and immunopeptidomes. inSPIRE boosts PSM identification rates in immunopeptidomics, leading to better performance than the original Prosit rescoring pipeline, as confirmed by benchmarking of inSPIRE performance on ground truth datasets. The integration of various features in the inSPIRE backbone further boosts the PSM identification in immunopeptidomics, with a potential benefit for the identification of noncanonical peptides.     

Calmodulin binds to Drosophila TRP with an unexpected mode

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Improving surface EMG burst detection in infrahyoid muscles during swallowing using digital filters and discrete wavelet analysis

The visual inspection is a widely used method for evaluating the surface electromyographic signal (sEMG) during deglutition, a process highly dependent of the examiners expertise. It is desirable to have a less subjective and automated technique to improve the onset detection in swallowing related muscles, which have a low signal-to-noise ratio. In this work, we acquired sEMG measured in infrahyoid muscles with high baseline noise of ten healthy adults during water swallowing tasks. Two methods were applied to find the combination of cutoff frequencies that achieve the most accurate onset detection: discrete wavelet decomposition based method and fixed steps variations of low and high cutoff frequencies of a digital bandpass filter. Teager-Kaiser Energy operator, root mean square and simple threshold method were applied for both techniques. Results show a narrowing of the effective bandwidth vs. the literature recommended parameters for sEMG acquisition. Both level 3 decomposition with mother wavelet db4 and bandpass filter with cutoff frequencies between 130 and 180 Hz were optimal for onset detection in infrahyoid muscles. The proposed methodologies recognized the onset time with predictive power above 0.95, that is similar to previous findings but in larger and more superficial muscles in limbs.     

Crop processing of <Emphasis Type="Italic">Olea europaea</Emphasis> L.: an experimental approach for the interpretation of archaeobotanical olive remains

Archaeobotanical research, ethnographic observations and laboratory experiments are put together to create model sequences of olive processing, which are developed, presented and explored as an aid for the interpretation of rich archaeobotanical assemblages of Olea. We conclude that the remains of different processing stages are reasonably distinctive in the archaeobotanical record and assist in the identification of different types of olive remains, such as fragmented olive stones, the inner kernels, and fruit flesh     

A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3′-processing and termination

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Comparison of whole‐genome (13X) and capture (87X) resequencing methods for SNP and genotype callings

The number of polymorphisms identified with next‐generation sequencing approaches depends directly on the sequencing depth and therefore on the experimental cost. Although higher levels of depth ensure more sensitive and more specific SNP calls, economic constraints limit the increase of depth for whole‐genome resequencing (WGS). For this reason, capture resequencing is used for studies focusing on only some specific regions of the genome. However, several biases in capture resequencing are known to have a negative impact on the sensitivity of SNP detection. Within this framework, the aim of this study was to compare the accuracy of WGS and capture resequencing on SNP detection and genotype calling, which differ in terms of both sequencing depth and biases. Indeed, we have evaluated the SNP calling and genotyping accuracy in a WGS dataset (13X) and in a capture resequencing dataset (87X) performed on 11 individuals. The percentage of SNPs not identified due to a sevenfold sequencing depth decrease was estimated at 7.8% using a down‐sampling procedure on the capture sequencing dataset. A comparison of the 87X capture sequencing dataset with the WGS dataset revealed that capture‐related biases were leading with the loss of 5.2% of SNPs detected with WGS. Nevertheless, when considering the SNPs detected by both approaches, capture sequencing appears to achieve far better SNP genotyping, with about 4.4% of the WGS genotypes that can be considered as erroneous and even 10% focusing on heterozygous genotypes. In conclusion, WGS and capture deep sequencing can be considered equivalent strategies for SNP detection, as the rate of SNPs not identified because of a low sequencing depth in the former is quite similar to SNPs missed because of method biases of the latter. On the other hand, capture deep sequencing clearly appears more adapted for studies requiring great accuracy in genotyping.     

Ecological parameters of the leaf‐litter frog community of an Atlantic Rainforest area at Ilha Grande,Rio de Janeiro state,Brazil

Abstract The Atlantic Rainforest originally covered much of the Brazilian coast and is now reduced to approximately only 7% of its original area. Data on abundance distribution and microhabitat characteristics of anuran amphibians living on the forest floor leaf litter in the Atlantic Rainforest are scarce. In this study, we analysed the effect of litter depth and structure on the abundance and species richness of leaf‐litter frogs in an area of Atlantic Rainforest at Ilha Grande, Rio de Janeiro State, south‐eastern Brazil. We performed monthly samples (nocturnal and diurnal) from August 1996 to October 1997 using small (2 m × 1 m) plots. We sampled 234 plots, totalling 468 m² of forest leaf litter. We estimated leaf‐litter depth and the proportion of leaves in the plot and tested their effect on the total abundance of frogs and species richness using multiple regression analysis. We found 185 frogs from eight species: Brachycephalus (=Psyllophryne) didactylus (Izecksohn, 1971) (Brachycephalidae), Dendrophryniscus brevipollicatus Jiménez de la Espada 1871 (Bufonidae), Adenomera marmorata Steindachner 1867, Eleutherodactylus parvus (Girard 1853), Eleutherodactylus guentheri (Steindachner 1864), Eleutherodactylus binotatus (Spix 1824) and Zachaenus parvulus (Girard 1853) (Leptodactylidae), and Chiasmocleis sp. (Microhylidae). Brachycephalus didactylus was the most abundant species, with 91 individuals, whereas Dendrophryniscus brevipollicatus was the rarest, with two individuals. Mean litter depth and the proportion of leaves in the leaf litter were significantly related to frog abundance (R² = 0.17; F_2,107 = 10.779; P = 0.0001) and species richness (R² = 0.11; F_2,107 = 6.375; P = 0.002) indicating that microhabitat characteristics may affect local distribution and abundance of frogs in the forest floor.     

Kinase-independent phosphoramidate S1P1 receptor agonist benzyl ether derivatives

Previously published S1P receptor modulator benzyl ether derivatives have shown potential as being viable therapeutics for the treatment of neurodegenerative diseases, however, two of the most S1P₁-selective compounds are reported as being poorly phosphorylated by kinases in vivo. Phosphoramidates of BED compounds (2a, 2b) were synthesised with the aim of producing kinase-independent S1P receptor modulators. Carboxypeptidase, human serum and cell lysate processing experiments were conducted. ProTide BED analogues were found to have an acceptable level of stability in acidic and basic conditions and in vitro metabolic processing experiments showed that they are processed to the desired pharmacologically active monophosphate. The research describes the development of an entirely novel family of therapeutic agents.