Multiple ancestries and shared gene flow among modern livestock guarding dogs.

Livestock guarding dogs (LGDs) have been used to protect livestock for millennia. While previous works suggested a single origin of modern LGDs, the degree and source of shared ancestry have not been tested. To address this, we generated genome-wide SNP data from 304 LGDs and combined it with public genomic data from 2,183 modern and 22 ancient dogs. Our findings reveal shared ancestry and extensive gene flow among modern LGD breeds which we attribute to historical livestock migrations. Additionally, admixture between LGDs and free-ranging dogs argues against reproductive isolation as a core mechanism for maintaining the specialized skills of LGDs. Finally, we identify two lineages within modern LGDs and uncover multiple ancestries tracing back to distinct Eurasian ancient dogs, concordant with the absence of a single ancestor. Overall, our work explores the complex evolutionary history of LGDs, offering valuable insights into how human and livestock co-migrations shaped this functional group.

Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies.

The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.

Characterization of the patterns of care, access, and direct cost of systemic lupus erythematosus in Brazil: findings from the Macunaíma study.

BACKGROUND: A cost of illness (COI) study aims to evaluate the socioeconomic burden that an illness imposes on society as a whole. This study aimed to describe the resources used, patterns of care, direct cost, and loss of productivity due to systemic lupus erythematosus (SLE) in Brazil. METHODS: This 12-month, cross-sectional, COI study of patients with SLE (ACR 1997 Classification Criteria) collected data using patient interviews (questionnaires) and medical records, covering: SLE profile, resources used, morbidities, quality of life (12-Item Short Form Survey, SF-12), and loss of productivity. Patients were excluded if they were retired or on sick leave for another illness. Direct resources included health-related (consultations, tests, medications, hospitalization) or non-health-related (transportation, home adaptation, expenditure on caregivers) hospital resources.Costs were calculated using the unit value of each resource and the quantity consumed. A gamma regression model explored cost predictors for patients with SLE. RESULTS: Overall, 300 patients with SLE were included (92.3% female,mean [standard deviation (SD)] disease duration 11.8 [7.9] years), of which 100 patients (33.3%) were on SLE-related sick leave and 46 patients (15.3%) had stopped schooling. Mean (SD) travel time from home to a care facility was 4.4 (12.6) hours. Antimalarials were the most commonly used drugs (222 [74.0%]). A negative correlation was observed between SF-12 physical component and SLE Disease Activity Index (- 0.117, p = 0.042), Systemic Lupus International CollaboratingClinics/AmericanCollegeofRheumatology Damage Index (- 0.115, p = 0.046), medications/day for multiple co-morbidities (- 0.272, p < 0.001), SLE-specific drugs/day (- 0.113, p = 0.051), and lost productivity (- 0.570, p < 0.001). For the mental component, a negative correlation was observed with medications/day for multiple co-morbidities (- 0.272, p < 0.001), SLE-specific medications/day (- 0.113, p = 0.051), and missed appointments (- 0.232, p < 0.001). Mean total SLE cost was US$3,123.53/patient/year (median [interquartile range (IQR)] US$1,618.51 [$678.66, $4,601.29]). Main expenditure was medication, with a median (IQR) cost of US$910.62 ($460, $4,033.51). Mycophenolate increased costs by 3.664 times (p < 0.001), and inflammatory monitoring (erythrocyte sedimentation rate or C-reactive protein) reduced expenditure by 0.381 times (p < 0.001). CONCLUSION: These results allowed access to care patterns, the median cost for patients with SLE in Brazil, and the differences across regions driven by biological, social, and behavioral factors. The cost of SLE provides an updated setting to support the decision-making process across the country.

RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control.

We present RawVegetable 2.0, a software tailored for assessing mass spectrometry data quality and fine-tuned for cross-linking mass spectrometry (XL-MS) applications. Building upon the capabilities of its predecessor, RawVegetable 2.0 introduces four main modules, each providing distinct and new functionalities: 1) Pair Finder, which identifies ion doublets characteristic of cleavable cross-linking experiments; 2) Diagnostic Peak Finder, which locates potential reporter ions associated with a specific cross-linker; 3) Precursor Signal Ratio, which computes the ratio between precursor intensity and the total signal in an MS/MS scan; and 4) Xrea, which evaluates spectral quality by analyzing the heterogeneity of peak intensities within a spectrum. These modules collectively streamline the process of optimizing mass spectrometry data acquisition for both Proteomics and XL-MS experiments. RawVegetable 2.0, along with a comprehensive tutorial is freely accessible for academic use at: http://patternlabforproteomics.org/rawvegetable2.

Characterization of the patterns of care, access, and direct cost of systemic lupus erythematosus in Brazil: findings from the Macunaíma study

Abstract Background A cost of illness (COI) study aims to evaluate the socioeconomic burden that an illness imposes on society as a whole. This study aimed to describe the resources used, patterns of care, direct cost, and loss of productivity due to systemic lupus erythematosus (SLE) in Brazil. Methods This 12-month, cross-sectional, COI study of patients with SLE (ACR 1997 Classification Criteria) collected data using patient interviews (questionnaires) and medical records, covering: SLE profile, resources used, morbidities, quality of life (12-Item Short Form Survey, SF-12), and loss of productivity. Patients were excluded if they were retired or on sick leave for another illness. Direct resources included health-related (consultations, tests, medications, hospitalization) or non-health-related (transportation, home adaptation, expenditure on caregivers) hospital resources. Costs were calculated using the unit value of each resource and the quantity consumed. A gamma regression model explored cost predictors for patients with SLE. Results Overall, 300 patients with SLE were included (92.3% female, mean [standard deviation (SD)] disease duration 11.8 [7.9] years), of which 100 patients (33.3%) were on SLE-related sick leave and 46 patients (15.3%) had stopped schooling. Mean (SD) travel time from home to a care facility was 4.4 (12.6) hours. Antimalarials were the most commonly used drugs (222 [74.0%]). A negative correlation was observed between SF-12 physical component and SLE Disease Activity Index (- 0.117, p = 0.042), Systemic Lupus International CollaboratingClinics/AmericanCollegeofRheumatology Damage Index (- 0.115, p = 0.046), medications/day for multiple co-morbidities (- 0.272, p < 0.001), SLE-specific drugs/day (- 0.113, p = 0.051), and lost productivity (- 0.570, p < 0.001). For the mental component, a negative correlation was observed with medications/day for multiple co-morbidities (- 0.272, p < 0.001), SLE-specific medications/day (- 0.113, p = 0.051), and missed appointments (- 0.232, p < 0.001). Mean total SLE cost was US$3,123.53/patient/year (median [interquartile range (IQR)] US$1,618.51 [$678.66, $4,601.29]). Main expenditure was medication, with a median (IQR) cost of US$910.62 ($460, $4,033.51). Mycophenolate increased costs by 3.664 times (p < 0.001), and inflammatory monitoring (erythrocyte sedimentation rate or C-reactive protein) reduced expenditure by 0.381 times (p < 0.001). Conclusion These results allowed access to care patterns, the median cost for patients with SLE in Brazil, and the differences across regions driven by biological, social, and behavioral factors. The cost of SLE provides an updated setting to support the decision-making process across the country.

Correlation between levels of perceived stress and depressive symptoms in the functional disability of patients with fibromyalgia.

OBJECTIVE: The aim of this study was to evaluate the factors that are most correlated with the levels of functional disability in patients with fibromyalgia. METHODS: This is a cross-sectional descriptive study in which 42 patients diagnosed with fibromyalgia according to the criteria of the American College of Rheumatology reported their status using the following questionnaires: the Beck Depression Inventory, the Perceived Stress Scale 14, the Revised Fibromyalgia Impact Questionnaire, the Visual Analog Pain Scale, and the Health Assessment Questionnaire. RESULTS: Moderate to severe levels of depression (Beck Depression Inventory: 22.35±10.39), moderate to severe functional disability (Health Assessment Questionnaire: 1.28±0.58), and high levels of stress (Perceived Stress Scale 14: 31.59±10.02) were found. The correlation adjusted by multiple regression as a function of the Health Assessment Questionnaire indicated a negligible to weak positive correlation with perceived stress (r=0.11), while a moderately strong positive correlation was observed with the Visual Analog Pain Scale (r=0.55). Regarding physical exercise, one of the pillars of the treatment, a moderate negative correlation was found with the Health Assessment Questionnaire (r=-0.4). CONCLUSION: The pain levels were moderately influenced by depression severity. The factors most linked to functional disability are due to the pain levels but not to the perception of stress.

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.

Over the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behaviour at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871). The metabolic model comprises 7871 genes, 6231 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen, with specific biomass compositions. The tissue-specific models were merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyse the pathways associated with the synthesis of suberin monomers, namely the acyl-lipids, phenylpropanoids, isoprenoids, and flavonoids production. The models developed in this work provide a systematic overview of the metabolism of Q. suber, including its secondary metabolism pathways and cork formation.

"Choose it, and remember it": The impact of choice on destination memory.

Destination memory can be defined as the capacity to remember to whom we transmit information. It is measured through the accuracy of retrieving the association between the information we transmit and the person to whom we transmit it. A destination memory procedure aims to emulate human interaction by sharing facts with celebrities (i.e., familiar faces) since we often communicate with people we know. However, the role of the choice about who we intend to transmit the information to has not been evaluated before. This paper investigated whether deciding with whom to share a piece of information benefits destination memory. We designed two experiments with different levels of cognitive load, increasing it from Experiment 1 to Experiment 2. The experiments included two conditions: the choice condition, in which participants chose from two options to whom they desired to share a fact, and the no-choice condition, in which participants simply shared facts with celebrities without the possibility of a choice. Experiment 1 suggested that a choice component did not affect destination memory. However, when in Experiment 2 we raised the cognitive load by increasing the number of stimuli, we found that selecting the recipient during the more challenging task provided an advantage in destination memory. This result is congruent with the explanation that the shift of the participants' attentional resources to the recipient, caused by the choice component, leads to a destination memory improvement. In sum, it seems that a choice component can improve destination memory only under demanding attentional conditions.

Shigella IpaA mediates actin bundling through diffusible vinculin oligomers with activation imprint.

Upon activation, vinculin reinforces cytoskeletal anchorage during cell adhesion. Activating ligands classically disrupt intramolecular interactions between the vinculin head and tail domains that bind to actin filaments. Here, we show that Shigella IpaA triggers major allosteric changes in the head domain, leading to vinculin homo-oligomerization. Through the cooperative binding of its three vinculin-binding sites (VBSs), IpaA induces a striking reorientation of the D1 and D2 head subdomains associated with vinculin oligomerization. IpaA thus acts as a catalyst producing vinculin clusters that bundle actin at a distance from the activation site and trigger the formation of highly stable adhesions resisting the action of actin relaxing drugs. Unlike canonical activation, vinculin homo-oligomers induced by IpaA appear to keep a persistent imprint of the activated state in addition to their bundling activity, accounting for stable cell adhesion independent of force transduction and relevant to bacterial invasion.

Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity.

Cross-linking mass spectrometry (XL-MS) is a universal tool for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental advances improved cross-link identification by enriching the cross-linker-modified peptides chemically with the use of enrichable cross-linkers. However, mono-links (i.e., peptides modified with a hydrolyzed cross-linker) still hinder efficient cross-link identification since a large proportion of measurement time is spent on their MS2 acquisition. Currently, cross-links and mono-links cannot be separated by sample preparation techniques or chromatography because they are chemically almost identical. Here, we found that based on the intensity ratios of four diagnostic peaks when using PhoX/tBu-PhoX cross-linkers, cross-links and mono-links can be partially distinguished. Harnessing their characteristic intensity ratios for real-time library search (RTLS)-based triggering of high-resolution MS2 scans increased the number of cross-link identifications from both single protein samples and intact E. coli cells. Specifically, RTLS improves cross-link identification from unenriched samples and short gradients, emphasizing its advantages in high-throughput approaches and when instrument time or sample amount is limited.

PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification.

Complex protein mixtures typically generate many tandem mass spectra produced by different peptides coisolated in the gas phase. Widely adopted proteomic data analysis environments usually fail to identify most of these spectra, succeeding at best in identifying only one of the multiple cofragmenting peptides. We present PatternLab V (PLV), an updated version of PatternLab that integrates the YADA 3 deconvolution algorithm to handle such cases efficiently. In general, we expect an increase of 10% in spectral identifications when dealing with complex proteomic samples. PLV is freely available at http://patternlabforproteomics.org.

Remembering to whom we transmit information during pandemics: the effect of face masks on destination memory.

Considering the global pandemic we currently experience, face masks have become standard in our daily routine. Even though surgical masks are established as a safety measure against the dissemination of COVID-19, previous research showed that their wearing compromises face recognition. Consequently, the capacity to remember to whom we transmit information-destination memory-could also be compromised. In our study, through a between-participants design (experiment 1) and a within-participants design (experiment 2), undergraduate students have to transmit Portuguese proverbs to masked and unmasked celebrity faces. Following our hypothesis, participants who shared information with masked faces had worse destination memory performance than those who shared information with unmasked faces. Also, we observed lower recognition for masked faces compared to unmasked faces. These results were expected since using a surgical mask affects facial recognition, thus making it harder to recognize a person to whom information was previously transmitted. More importantly, these results also support the idea that variables associated with the recipient's face are important for destination memory performance.

DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters.

MOTIVATION: There are several well-established paradigms for identifying and pinpointing discriminative peptides/proteins using shotgun proteomic data; examples are peptide-spectrum matching, de novo sequencing, open searches, and even hybrid approaches. Such an arsenal of complementary paradigms can provide deep data coverage, albeit some unidentified discriminative peptides remain. RESULTS: We present DiagnoMass, software tool that groups similar spectra into spectral clusters and then shortlists those clusters that are discriminative for biological conditions. DiagnoMass then communicates with proteomic tools to attempt the identification of such clusters. We demonstrate the effectiveness of DiagnoMass by analyzing proteomic data from Escherichia coli, Salmonella, and Shigella, listing many high-quality discriminative spectral clusters that had thus far remained unidentified by widely adopted proteomic tools. DiagnoMass can also classify proteomic profiles. We anticipate the use of DiagnoMass as a vital tool for pinpointing biomarkers. AVAILABILITY: DiagnoMass and related documentation, including a usage protocol, are available at http://www.diagnomass.com.

Correlation between levels of perceived stress and depressive symptoms in the functional disability of patients with fibromyalgia

SUMMARY OBJECTIVE: The aim of this study was to evaluate the factors that are most correlated with the levels of functional disability in patients with fibromyalgia. METHODS: This is a cross-sectional descriptive study in which 42 patients diagnosed with fibromyalgia according to the criteria of the American College of Rheumatology reported their status using the following questionnaires: the Beck Depression Inventory, the Perceived Stress Scale 14, the Revised Fibromyalgia Impact Questionnaire, the Visual Analog Pain Scale, and the Health Assessment Questionnaire. RESULTS: Moderate to severe levels of depression (Beck Depression Inventory: 22.35±10.39), moderate to severe functional disability (Health Assessment Questionnaire: 1.28±0.58), and high levels of stress (Perceived Stress Scale 14: 31.59±10.02) were found. The correlation adjusted by multiple regression as a function of the Health Assessment Questionnaire indicated a negligible to weak positive correlation with perceived stress (r=0.11), while a moderately strong positive correlation was observed with the Visual Analog Pain Scale (r=0.55). Regarding physical exercise, one of the pillars of the treatment, a moderate negative correlation was found with the Health Assessment Questionnaire (r=-0.4). CONCLUSION: The pain levels were moderately influenced by depression severity. The factors most linked to functional disability are due to the pain levels but not to the perception of stress.

Two New Species of Backusella (Mucorales, Mucoromycota) from Soil in an Upland Forest in Northeastern Brazil with an Identification Key of Backusella from the Americas.

During a survey of Mucorales from a forest located in Pernambuco state, Brazil, two new Backusella species were discovered and described based on morphological and molecular data (internal transcribed spacer and large subunit ribosomal DNA sequences). Both species were characterized as unbranched sporangiophores and sporangia with columellae of varied shapes forming. Multispored sporangiola were frequent, whereas unispored sporangiola were rare. URM 8395 forms sporangiophores that may support hyaline, slightly curved or circinate pedicels with multispored sporangiola at their apical portion, and abundant giant cells and chlamydospores. Columellae of sporangia are hyaline, conical (majority), or ellipsoidal with a truncate base, globose to subglobose or subglobose to conical, and, rarely, with slight medial constriction. URM 8427 does not form sporangiola from pedicels, giant cells are not observed, and columellae of sporangia are globose to subglobose, cylindrical with a truncate base, some with a slight constriction, applanate, obovoid, ellipsoidal, or, rarely, conical. Some columellae may have one side more swollen than the other and some are arranged obliquely on the sporangiophores. Sterile sporangia may or may not be formed on short sporophores. The detailed description and illustration of both novel species as well as an identification key for Backusella from the Americas are provided.

Increasing confidence in proteomic spectral deconvolution through mass defect.

MOTIVATION: Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra. RESULTS: In general, all deconvolution algorithms may eventually report mass peaks that are not compatible with the chemical formula of any peptide. We show how to remove these artifacts by considering their mass defects. We introduce Y.A.D.A. 3.0, a fast deconvolution algorithm that can remove peaks with unacceptable mass defects. Our approach is effective for polypeptides with less than 10 kDa, and its essence can be easily incorporated into any deconvolution algorithm. AVAILABILITY AND IMPLEMENTATION: Y.A.D.A. 3.0 is freely available for academic use at http://patternlabforproteomics.org/yada3. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models.

Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms' metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models' reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.

Simple, efficient and thorough shotgun proteomic analysis with PatternLab V.

Shotgun proteomics aims to identify and quantify the thousands of proteins in complex mixtures such as cell and tissue lysates and biological fluids. This approach uses liquid chromatography coupled with tandem mass spectrometry and typically generates hundreds of thousands of mass spectra that require specialized computational environments for data analysis. PatternLab for proteomics is a unified computational environment for analyzing shotgun proteomic data. PatternLab V (PLV) is the most comprehensive and crucial update so far, the result of intensive interaction with the proteomics community over several years. All PLV modules have been optimized and its graphical user interface has been completely updated for improved user experience. Major improvements were made to all aspects of the software, ranging from boosting the number of protein identifications to faster extraction of ion chromatograms. PLV provides modules for preparing sequence databases, protein identification, statistical filtering and in-depth result browsing for both labeled and label-free quantitation. The PepExplorer module can even pinpoint de novo sequenced peptides not already present in the database. PLV is of broad applicability and therefore suitable for challenging experimental setups, such as time-course experiments and data handling from unsequenced organisms. PLV interfaces with widely adopted software and community initiatives, e.g., Comet, Skyline, PEAKS and PRIDE. It is freely available at http://www.patternlabforproteomics.org .

Optimized TMT-Based Quantitative Cross-Linking Mass Spectrometry Strategy for Large-Scale Interactomic Studies.

Cross-linking mass spectrometry (XL-MS) is a powerful method for the investigation of protein-protein interactions (PPI) from highly complex samples. XL-MS combined with tandem mass tag (TMT) labeling holds the promise of large-scale PPI quantification. However, a robust and efficient TMT-based XL-MS quantification method has not yet been established due to the lack of a benchmarking dataset and thorough evaluation of various MS parameters. To tackle these limitations, we generate a two-interactome dataset by spiking in TMT-labeled cross-linked Escherichia coli lysate into TMT-labeled cross-linked HEK293T lysate using a defined mixing scheme. Using this benchmarking dataset, we assess the efficacy of cross-link identification and accuracy of cross-link quantification using different MS acquisition strategies. For identification, we compare various MS2- and MS3-based XL-MS methods, and optimize stepped higher energy collisional dissociation (HCD) energies for TMT-labeled cross-links. We observed a need for notably higher fragmentation energies compared to unlabeled cross-links. For quantification, we assess the quantification accuracy and dispersion of MS2-, MS3-, and synchronous precursor selection-MS3-based methods. We show that a stepped HCD-MS2 method with stepped collision energies 36-42-48 provides a vast number of quantifiable cross-links with high quantification accuracy. This widely applicable method paves the way for multiplexed quantitative PPI characterization from complex biological systems.

TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics.

MOTIVATION: We present a new software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS (tandem mass spectrometry) analysis of intact proteins. Our tool can process data obtained from various deconvolution and fragment assignment software. RESULTS: We demonstrate that TDFragMapper can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics. AVAILABILITY AND IMPLEMENTATION: TDFragMapper, a demonstration video and user tutorial are freely available for academic use at https://msbio.pasteur.fr/tdfragmapper; all data are thus available from the ProteomeXchange consortium (identifier PXD024643). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.