Cocoa by-product inclusion in dairy sheep diet: effect on sensory, volatile and antioxidant properties of cheese

The possibility of inclusion of agro-industrial by-products in the diet of small ruminants represents both an economical and an environmental strategy for reducing waste management by industries and the cost of feeding as well as the impact of livestock farming. Large amounts of wastes from the cocoa industry are annually produced with a considerable part represented by cocoa bean shells, considered a suitable ingredient to be included in the diet of ruminants within the limits established by European legislation. The aim of this study was to assess the effect of including cocoa bean shells in the diet of dairy sheep on the sensory, volatile, and antioxidant properties of cheese. To this purpose, 20 Comisana lactating ewes were randomly assigned to 2 experimental groups: control (CTRL) and cocoa bean shells (CBS), and received alfalfa hay ad libitum and 800g of conventional (CTRL) or experimental (CBS) concentrate containing 11.7% CBS to partially replace corn and barley of the CTRL concentrate. Bulk milk collected from each group was used to produce a total of 15 cheeses per group, obtained in 5 different days of cheese-making (3 cheeses a day per group). After 60 d of aging, each cheese of each experimental group was sampled for the analyses. The results on chemical composition revealed a greater monounsaturated fatty acids content and an increase in the nutritional indices suggesting a favorable role of cocoa bean shells dietary inclusion on the nutritive value of the cheese. The cheese sensory profile was affected by the cocoa bean shells inclusion, with more pronounced appearance, odor, aroma, and taste attributes in the product. The volatile profile showed only a few significant differences, mainly related to the cheese ripening process, and no differences were found in α-tocopherol contents in cheese fat between the 2 groups. Therefore, the coca bean shells inclusion in the diet of dairy sheep allowed to obtain a good quality cheese, without altering the characteristics associated with the typical profiles of sheep cheese. Furthermore, the use of this by-product could contribute to decrease feed costs and waste management, representing a good practice for increasing the sustainability of dairy products.

A pgr5 suppressor screen uncovers two distinct suppression mechanisms and links cytochrome b6f complex stability to PGR5

PROTON GRADIENT REGULATION5 (PGR5) is thought to promote cyclic electron flow, and its deficiency impairs photosynthetic control and increases photosensitivity of photosystem (PS) I, leading to seedling lethality under fluctuating light (FL). By screening for Arabidopsis (Arabidopsis thaliana) suppressor mutations that rescue the seedling lethality of pgr5 plants under FL, we identified a portfolio of mutations in 12 different genes. These mutations affect either PSII function, cytochrome b6f (cyt b6f) assembly, plastocyanin (PC) accumulation, the CHLOROPLAST FRUCTOSE-1,6-BISPHOSPHATASE1 (cFBP1), or its negative regulator ATYPICAL CYS HIS-RICH THIOREDOXIN2 (ACHT2). The characterization of the mutants indicates that the recovery of viability can in most cases be explained by the restoration of PSI donor side limitation, which is caused by reduced electron flow to PSI due to defects in PSII, cyt b6f, or PC. Inactivation of cFBP1 or its negative regulator ACHT2 results in increased levels of the NADH dehydrogenase-like complex. This increased activity may be responsible for suppressing the pgr5 phenotype under FL conditions. Plants that lack both PGR5 and DE-ETIOLATION-INDUCED PROTEIN1 (DEIP1)/NEW TINY ALBINO1 (NTA1), previously thought to be essential for cyt b6f assembly, are viable and accumulate cyt b6f. We suggest that PGR5 can have a negative effect on the cyt b6f complex and that DEIP1/NTA1 can ameliorate this negative effect.

NTRC and thioredoxins m1/m2 underpin the light acclimation of plants on proteome and metabolome levels

During photosynthesis, plants must manage strong fluctuations in light availability on different time scales, leading to long-term acclimation and short-term responses. However, little is known about the regulation and coordination of these processes and the modulators involved. In this study, we used proteomics, metabolomics, and reverse genetics to investigate how different light environmental factors, such as intensity or variability, affect long-term and short-term acclimation responses of Arabidopsis (Arabidopsis thaliana) and the importance of the chloroplast redox network in their regulation. In the wild type, high light, but not fluctuating light, led to large quantitative changes in the proteome and metabolome, accompanied by increased photosynthetic dynamics and plant growth. This finding supports light intensity as a stronger driver for acclimation than variability. Deficiencies in NADPH-thioredoxin reductase C (NTRC) or thioredoxins m1/m2, but not thioredoxin f1, almost completely suppressed the re-engineering of the proteome and metabolome, with both the induction of proteins involved in stress and redox responses and the repression of those involved in cytosolic and plastid protein synthesis and translation being strongly attenuated. Moreover, the correlations of protein or metabolite levels with light intensity were severely disturbed, suggesting a general defect in the light-dependent acclimation response, resulting in impaired photosynthetic dynamics. These results indicate a previously unknown role of NTRC and thioredoxins m1/m2 in modulating light acclimation at proteome and metabolome levels to control dynamic light responses. NTRC, but not thioredoxins m1/m2 or f1, also improves short-term photosynthetic responses by balancing the Calvin-Benson cycle in fluctuating light.

NTRC regulates CP12 to activate Calvin-Benson cycle during cold acclimation

NADPH-dependent thioredoxin reductase C (NTRC) is a chloroplast redox regulator in algae and plants. Here, we used site-specific mutation analyses of the thioredoxin domain active site of NTRC in the green alga Chlamydomonas reinhardtii to show that NTRC mediates cold tolerance in a redox-dependent manner. By means of coimmunoprecipitation and mass spectrometry, a redox- and cold-dependent binding of the Calvin-Benson Cycle Protein 12 (CP12) to NTRC was identified. NTRC was subsequently demonstrated to directly reduce CP12 of C. reinhardtii as well as that of the vascular plant Arabidopsis thaliana in vitro. As a scaffold protein, CP12 joins the Calvin-Benson cycle enzymes phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to form an autoinhibitory supracomplex. Using size-exclusion chromatography, NTRC from both organisms was shown to control the integrity of this complex in vitro and thereby PRK and GAPDH activities in the cold. Thus, NTRC apparently reduces CP12, hence triggering the dissociation of the PRK/CP12/GAPDH complex in the cold. Like the ntrc::aphVIII mutant, CRISPR-based cp12::emx1 mutants also exhibited a redox-dependent cold phenotype. In addition, CP12 deletion resulted in robust decreases in both PRK and GAPDH protein levels implying a protein protection effect of CP12. Both CP12 functions are critical for preparing a repertoire of enzymes for rapid activation in response to environmental changes. This provides a crucial mechanism for cold acclimation.

A bench-top Dark-Root device built with LEGO® bricks enables a non-invasive plant root development analysis in soil conditions mirroring nature

Roots are the hidden parts of plants, anchoring their above-ground counterparts in the soil. They are responsible for water and nutrient uptake and for interacting with biotic and abiotic factors in the soil. The root system architecture (RSA) and its plasticity are crucial for resource acquisition and consequently correlate with plant performance while being highly dependent on the surrounding environment, such as soil properties and therefore environmental conditions. Thus, especially for crop plants and regarding agricultural challenges, it is essential to perform molecular and phenotypic analyses of the root system under conditions as near as possible to nature (#asnearaspossibletonature). To prevent root illumination during experimental procedures, which would heavily affect root development, Dark-Root (D-Root) devices (DRDs) have been developed. In this article, we describe the construction and different applications of a sustainable, affordable, flexible, and easy to assemble open-hardware bench-top LEGO® DRD, the DRD-BIBLOX (Brick Black Box). The DRD-BIBLOX consists of one or more 3D-printed rhizoboxes, which can be filled with soil while still providing root visibility. The rhizoboxes sit in a scaffold of secondhand LEGO® bricks, which allows root development in the dark and non-invasive root tracking with an infrared (IR) camera and an IR light-emitting diode (LED) cluster. Proteomic analyses confirmed significant effects of root illumination on barley root and shoot proteomes. Additionally, we confirmed the significant effect of root illumination on barley root and shoot phenotypes. Our data therefore reinforces the importance of the application of field conditions in the lab and the value of our novel device, the DRD-BIBLOX. We further provide a DRD-BIBLOX application spectrum, spanning from investigating a variety of plant species and soil conditions and simulating different environmental conditions and stresses, to proteomic and phenotypic analyses, including early root tracking in the dark.

Seven years of studying the associations between political polarization and problematic information: a literature review

This literature review examines the intersection between political polarization and problematic information, two phenomena prominent in recent events like the 2016 Trump election and the 2020 COVID-19 pandemic. We analyzed 68 studies out of over 7,000 records using quantitative and qualitative methods. Our review revealed a lack of research on the relationship between political polarization and problematic information and a shortage of theoretical consideration of these phenomena. Additionally, US samples and Twitter and Facebook were frequently analyzed. The review also found that surveys and experiments were commonly used, with polarization significantly predicting problematic information consumption and sharing.

Hematocolpos due to imperforate hymen: a case report and literature systematic review

INTRODUCTION AND HYPOTHESIS

Hematocolpos is a rare condition, where menstrual blood fills the vagina, instead of being expelled, due to a series of uterovaginal pathologies, the most frequent of which is the imperforate hymen. To date, few cases of hematocolpos have been reported in the literature.

METHODS

We report a case of hematometrocolpos due to imperforate hymen initially misdiagnosed as constipation and subsequently as ovarian mass; moreover, the present study undertakes a systematic review of studies on hematometrocolpos due to imperforate hymen to synthesize available knowledge on epidemiology, diagnosis, and management about this rare condition.

RESULTS

A total of 35 studies, describing 61 patients, were identified. The presence of hematocolpos should be suspected in premenarchal patients complaining of low abdominal pain, abdominal swelling, and urinary retention. Genital examination disclosing a tender, pale hymen and ultrasound represent a useful tool for diagnosis. The goal of the management is to timely perform hymenotomy to drain the hematocolpos, followed by hymenectomy to prevent recurrence. Follow-up is needed to diagnose possible recurrences.

CONCLUSIONS

In the case of an adolescent girl complaining of genital pain associated with primary amenorrhea, hematocolpos due to imperforate hymen should be suspected.

CGL160-mediated recruitment of the coupling factor CF1 is required for efficient thylakoid ATP synthase assembly, photosynthesis, and chloroplast development in Arabidopsis

Chloroplast ATP synthases consist of a membrane-spanning coupling factor (CFO) and a soluble coupling factor (CF1). It was previously demonstrated that CONSERVED ONLY IN THE GREEN LINEAGE160 (CGL160) promotes the formation of plant CFO and performs a similar function in the assembly of its c-ring to that of the distantly related bacterial Atp1/UncI protein. Here, we show that in Arabidopsis (Arabidopsis thaliana) the N-terminal portion of CGL160 (AtCGL160N) is required for late steps in CF1-CFO assembly. In plants that lacked AtCGL160N, CF1-CFO content, photosynthesis, and chloroplast development were impaired. Loss of AtCGL160N did not perturb c-ring formation, but led to a 10-fold increase in the numbers of stromal CF1 subcomplexes relative to that in the wild type. Co-immunoprecipitation and protein crosslinking assays revealed an association of AtCGL160 with CF1 subunits. Yeast two-hybrid assays localized the interaction to a stretch of AtCGL160N that binds to the DELSEED-containing CF1-β subdomain. Since Atp1 of Synechocystis (Synechocystis sp. PCC 6803) could functionally replace the membrane domain of AtCGL160 in Arabidopsis, we propose that CGL160 evolved from a cyanobacterial ancestor and acquired an additional function in the recruitment of a soluble CF1 subcomplex, which is critical for the modulation of CF1-CFO activity and photosynthesis.

Commonalities and specialties in photosynthetic functions of PROTON GRADIENT REGULATION5 variants in Arabidopsis

The PROTON GRADIENT REGULATION5 (PGR5) protein is required for trans-thylakoid proton gradient formation and acclimation to fluctuating light (FL). PGR5 functionally interacts with two other thylakoid proteins, PGR5-like 1 (PGRL1) and 2 (PGRL2); however, the molecular details of these interactions are largely unknown. In the Arabidopsis (Arabidopsis thaliana) pgr5-1 mutant, the PGR5G130S protein accumulates in only small amounts. In this work, we generated a knockout allele of PGR5 (pgr5-Cas) using CRISPR-Cas9 technology. Like pgr5-1, pgr5-Cas is seedling-lethal under FL, but photosynthesis and particularly cyclic electron flow, as well as chlorophyll content, are less severely affected in both pgr5-Cas and pgrl1ab (which lacks PGRL1 and PGR5) than in pgr5-1. These differences are associated with changes in the levels of 260 proteins, including components of the Calvin-Benson cycle, photosystems II and I, and the NDH complex, in pgr5-1 relative to the wild type (WT), pgr5-Cas, and pgrl1ab. Some of the differences between pgr5-1 and the other mutant lines could be tentatively assigned to second-site mutations in the pgr5-1 line, identified by whole-genome sequencing. However, others, particularly the more pronounced photosynthetic defects and PGRL1 depletion (compared to pgr5-Cas), are clearly due to specific negative effects of the amino-acid substitution in PGR5G130S, as demonstrated by complementation analysis. Moreover, pgr5-1 and pgr5-Cas plants are less tolerant to long-term exposure to high light than pgrl1ab plants. These results imply that, in addition to the previously reported necessity of PGRL1 for optimal PGR5 function, PGR5 is required alongside PGRL1 to avoid harmful effects on plant performance.

Mast Cell Tumour and Mammary Gland Carcinoma Collision Tumour. Case report and literature review

Collision tumours are the coexistence, at the same venue, of distinct tumours not macroscopically distinguishable and consisting of two independent cell populations without histological admixture. In human medicine, collision tumours in different anatomical sites have been described. In the veterinary literature, few cases exist so far. A 12-year-old female Labrador with a mammary gland nodular lesion was presented for clinical examination. The nodule was surgically removed and underwent histological and immunohistochemical analysis. Histopathological examination revealed two distinct malignant tumours: a mammary gland carcinoma and a cutaneous mast cells tumour. To the author's knowledge, the paper reports the first case of a collision tumour composed of mammary gland neoplasia and mast cell tumour. The rising interest in collision tumours suggests widening their knowledge and setting up a multimodal approach that includes surgery and targeted therapy.

An ancient function of PGR5 in iron delivery?

In all phototrophic organisms, the photosynthetic apparatus must be protected from light-induced damage. One important mechanism that mitigates photodamage in plants is antimycin A (AA)-sensitive cyclic electron flow (CEF), the evolution of which remains largely obscure. Here we show that proton gradient regulation 5 (PGR5), a key protein involved in AA-sensitive CEF, displays intriguing commonalities - including sequence and structural features - with a group of ferritin-like proteins. We therefore propose that PGR5 may originally have been involved in prokaryotic iron mobilization and delivery, which facilitated a primordial type of CEF as a side effect. The abandonment of the bacterioferritin system during the transformation of cyanobacterial endosymbionts into chloroplasts might have allowed PGR5 to functionally specialize in CEF.

Rapid quasi-periodic oscillations in the relativistic jet of BL Lacertae

Blazars are active galactic nuclei (AGN) with relativistic jets whose non-thermal radiation is extremely variable on various timescales^1-3. This variability seems mostly random, although some quasi-periodic oscillations (QPOs), implying systematic processes, have been reported in blazars and other AGN. QPOs with timescales of days or hours are especially rare⁴ in AGN and their nature is highly debated, explained by emitting plasma moving helically inside the jet⁵, plasma instabilities^6,7 or orbital motion in an accretion disc^7,8. Here we report results of intense optical and γ-ray flux monitoring of BL Lacertae (BL Lac) during a dramatic outburst in 2020 (ref. ⁹). BL Lac, the prototype of a subclass of blazars¹⁰, is powered by a 1.7 × 10⁸ M_Sun (ref. ¹¹) black hole in an elliptical galaxy (distance = 313 megaparsecs (ref. ¹²)). Our observations show QPOs of optical flux and linear polarization, and γ-ray flux, with cycles as short as approximately 13 h during the highest state of the outburst. The QPO properties match the expectations of current-driven kink instabilities⁶ near a recollimation shock about 5 parsecs (pc) from the black hole in the wake of an apparent superluminal feature moving down the jet. Such a kink is apparent in a microwave Very Long Baseline Array (VLBA) image.

P86 IN–HOSPITAL OUTCOMES OF PORTICO TRANSCATHETER AORTIC VALVE IMPLANTATION WITH THE FLEXNAV AS COMPARED TO THE FIRST–GENERATION DELIVERY SYSTEM

Introduction

technological advancements in transcatheter heart valve platforms, along with increasing operator experience and careful patient selection, are essential to reach high standards of efficacy and safety in transcatheter aortic valve replacement (TAVR). Aim of this study was to evaluate the performance of the new version of the Portico valve delivery system (FlexNav) as compared to the first–generation device.

Materials and Methods

we report the results of a single–center, observational study on patients with severe aortic valve stenosis undergoing TAVR with the Portico valve at our Institution. Consecutive patients treated with the new FlexNav delivery system (DS), available since May, 2020, were compared with patients treated with the first–generation delivery system (1st Gen–DS). In–hospital outcomes were self–adjudicated according to the Valve Academic Research Consortium–3 definition.

Results

50 patients were included in this study; 22 were treated with the FlexNav–DS and the remaining with the 1st Gen–DS. Clinical characteristics were similar between group, expect for older age (82.6 ± 3.6 vs 80.7 ± 3.8; p = 0.07) and higher prevalence of female gender (68.2% vs 39.3%; p = 0.04) in FlexNav–DS group as compared to 1st Gen–DS group, respectively. We observed similar rates of procedural success but higher rate of moderate–to–severe paravalvular leak in 1st Gen–DS as compared to FlexNav–DS group (28.6% vs 4.6%; p = 0.03); major vascular complications were reduced, although not significantly, in the FlexNav–DS as compared to 1st Gen–DS group (4.5% vs 10.7%; p = 0.64).

Conclusion

Our data suggest that the FlexNav DS, thanks to lower profile and enhanced stability during valve deployment, has the potential to allow for to better procedural and clinical results of TAVR with the Portico valve as compared to the 1st Gen–DS.

Device therapy for the major complications detection and early treatment of patients with natural and iatrogenic comorbidities admitted to internal medicine wards

Background

Whith advances in devices miniaturization and wireless technologies, wereable “on body” ECG patch devices are unobtrusive and easy to use. Continuous ECG monitoring in the short term is indicated in patients who, due to age, comorbidities and polytherapy, are at greater risk of arrhythmias. Since 2017, a randomized-open label study is being conducted at the admission of acute patients in Internal Medicine Unit for 72 hours with continuous monitoring of vital parameters and the 5 leads-ECG (VP-ECG CM) trace by the mean of a tele-cardiology program.

Purpose

Objective of this study is to perform a cost-effectiveness evaluation of the VP-ECG CM program in inpatient settings.

Methods

Data were used in order to evaluate costs, the program effectiveness and the QALY gains using wireless monitoring compared to nurses traditional one. Costs were estimated by mean of the identification, measuring and valorization of the resources uptake. Cost drivers included: time spent by personnel, cost of the device, consumables, medical treatments, diagnostic exams and complications. The perspective of the Italian National Health Service was adopted. The incremental analysis was performed in order to present the cost per complication avoided and the cost per QALY gained. Net monetary benefit was also calculated. Either a deterministic and probabilistic analysis were performed by means of a bootstrap simulation allowing for re-sampling. A cost-effectiveness-acceptability curve was estimated, considering a cost-effectiveness threshold of €35,000/QALY.

Results

On 143 patients, arrhythmias and acute coronary syndrome were detected 4.3% in the experimental arm and 1.9% in the control arm, whilst 29,5% major complications were detected in the experimental arm vs 43.5% in the control and reduction in the number of sudden deaths (16% control and 9.3% experimental). Time spent by nurses in the control arm (58 minutes/day/patient) was the most relevant cost driver and allowed a saving ranging €54–90/patient. This saving overwhelmed the costs for the equipment whilst the other costs remained unchanged, thus allowing for the VP-ECG CM to be dominant versus the standard of care. One way and multiway sensitivity analyses confirmed the robustness of our results with p-value 0,05 involved in the bootstrap presenting dominance of the VP-ECG CM.

Conclusions

Notwithstanding the concerns of a loss of control in patient management, telemedicine (digital health infrastructure and driver) could perform healthcare transformation enabling physicians to increase the volume of patients seen, reduce the time to diagnosis, improve efficiency and efficacy of disease management, and reduce unnecessary clinic visits and hospital admissions. The miniaturized technologies can improve patient adherence, and the detection, characterization and monitoring of cardiac arrhythmias – readily digitalized markers and phenotypes of cardiovascular disease.

Funding Acknowledgement

Type of funding sources: None. Wireless Monitoring Study flowchart

Constant rate infusion of tramadol in isoflurane-anesthetized pigs undergoing experimental surgery

The purpose of this study was to investigate the effect of tramadol (TM) (2 mg/kg) administered intramuscularly (IM) followed by a constant rate infusion (CRI) of TM (2 mg/kg/h) in pigs. Sixteen pigs undergoing experimental surgery were premedicated IM with a combination of alfaxalone (5 mg/kg) and midazolam (0.5 mg/kg). Anaesthesia was induced with propofol (2 mg/kg) intravenously (IV) and maintained with isoflurane. Pigs were randomly assigned to one of the two following groups: Group 1 (n=8): received a loading dose of TM (2 mg/kg) followed by a CRI of TM (2 mg/kg/h); Group 2 (n=8): a loading dose of TM (2 mg/kg) followed by a CRI of lactated Ringer's solution (2 ml/kg/h). Heart rate (HR), respiratory rate (RR), rectal temperature (RT), haemoglobin oxygen saturation (SpO2), fraction of inspired oxygen (FIO2), end-tidal concentration of isoflurane (FEISO), end-tidal carbon dioxide concentration (FECO2), pH, arterial oxygen partial pressure (PaO2), arterial carbon dioxide partial pressure (PaCO2) and bicarbonate concentration (HCO3-) were recorded immediately after loss of righting reflex (T=0 min) and at 15-min intervals over a period of 60 min. Continuous data were analysed using a repeated- -measure analysis of variance (ANOVA) and a p-value ⟨0.05 was considered significant. HR, RR and FEISO were significantly lower (p⟨0.05) in Group 1 at T30 and T45, which corresponded to the time of the most intense surgical stimulation. The results suggest that the TM infusion minimizes the HR and RR response, slightly reducing isoflurane requirements and determining a superior perioperative analgesia.

Gene Replacement in Arabidopsis Reveals Manganese Transport as an Ancient Feature of Human, Plant and Cyanobacterial UPF0016 Proteins

The protein family 0016 (UPF0016) is conserved through evolution, and the few members characterized share a function in Mn²⁺ transport. So far, little is known about the history of these proteins in Eukaryotes. In Arabidopsis thaliana five such proteins, comprising four different subcellular localizations including chloroplasts, have been described, whereas non-photosynthetic Eukaryotes have only one. We used a phylogenetic approach to classify the eukaryotic proteins into two subgroups and performed gene-replacement studies to investigate UPF0016 genes of various origins. Replaceability can be scored readily in the Arabidopsis UPF0016 transporter mutant pam71, which exhibits a functional deficiency in photosystem II. The N-terminal region of the Arabidopsis PAM71 was used to direct selected proteins to chloroplast membranes. Transgenic pam71 lines overexpressing the closest plant homolog (CMT1), human TMEM165 or cyanobacterial MNX successfully restored photosystem II efficiency, manganese binding to photosystem II complexes and consequently plant growth rate and biomass production. Thus AtCMT1, HsTMEM165, and SynMNX can operate in the thylakoid membrane and substitute for PAM71 in a non-native environment, indicating that the manganese transport function of UPF0016 proteins is an ancient feature of the family. We propose that the two chloroplast-localized UPF0016 proteins, CMT1 and PAM71, in plants originated from the cyanobacterial endosymbiont that gave rise to the organelle.

Systems biology of responses to simultaneous copper and iron deficiency in Arabidopsis

Plant responses to coincident nutrient deficiencies cannot be predicted from the responses to individual deficiencies. Although copper (Cu) and iron (Fe) are essential micronutrients for plant growth that are often and concurrently limited in soils, the combinatorial response to Cu-Fe deficiency remains elusive. In the present study, we characterised the responses of Arabidopsis thaliana plants deprived of Cu, Fe or both (-Cu-Fe) at the level of plant development, mineral composition, and reconfiguration of transcriptomes, proteomes and metabolomes. Compared to single deficiencies, simultaneous -Cu-Fe leads to a distinct pattern in leaf physiology and microelement concentration characterised by lowered protein content and enhanced manganese and zinc levels. Conditional networking analysis of molecular changes indicates that biological processes also display different co-expression patterns among single and double deficiencies. Indeed, the interaction between Cu and Fe deficiencies causes distinct expression profiles for 15% of all biomolecules, leading to specific enhancement of general stress responses and protein homeostasis mechanisms, at the same time as severely arresting photosynthesis. Accordingly, central carbon metabolites, in particular photosynthates, decrease especially under -Cu-Fe conditions, whereas the pool of free amino acids increases. Further meta-analysis of transcriptomes and proteomes corroborated that protein biosynthesis and folding capacity were readjusted during the combinatorial response and unveiled important rearrangements in the metabolism of organic acids. Consequently, our results demonstrate that the response to -Cu-Fe imposes a distinct reconfiguration of large sets of molecules, not triggered by single deficiencies, resulting into a switch from autotrophy to heterotrophy and involving organic acids such as fumaric acid as central mediators of the response.

The Arabidopsis Protein CGL20 Is Required for Plastid 50S Ribosome Biogenesis

Biogenesis of plastid ribosomes is facilitated by auxiliary factors that process and modify ribosomal RNAs (rRNAs) or are involved in ribosome assembly. In comparison with their bacterial and mitochondrial counterparts, the biogenesis of plastid ribosomes is less well understood, and few auxiliary factors have been described so far. In this study, we report the functional characterization of CONSERVED ONLY IN THE GREEN LINEAGE20 (CGL20) in Arabidopsis (Arabidopsis thaliana; AtCGL20), which is a Pro-rich, ∼10-kD protein that is targeted to mitochondria and chloroplasts. In Arabidopsis, CGL20 is encoded by segmentally duplicated genes of high sequence similarity (AtCGL20A and AtCGL20B). Inactivation of these genes in the atcgl20ab mutant led to a visible virescent phenotype and growth arrest at low temperature. The chloroplast proteome, pigment composition, and photosynthetic performance were significantly affected in atcgl20ab mutants. Loss of AtCGL20 impaired plastid translation, perturbing the formation of a hidden break in the 23S rRNA and causing abnormal accumulation of 50S ribosomal subunits in the high-molecular-mass fraction of chloroplast stromal extracts. Moreover, AtCGL20A-eGFP fusion proteins comigrated with 50S ribosomal subunits in Suc density gradients, even after RNase treatment of stromal extracts. Therefore, we propose that AtCGL20 participates in the late stages of the biogenesis of 50S ribosomal subunits in plastids, a role that presumably evolved in the green lineage as a consequence of structural divergence of plastid ribosomes.

Polarization dependence of second harmonic generation from plasmonic nanoprism arrays

The second order nonlinear optical response of gold nanoprisms arrays is investigated by means of second harmonic generation (SHG) experiments and simulations. The polarization dependence of the nonlinear response exhibits a 6-fold symmetry, attributed to the local field enhancement through the excitation of the surface plasmon resonances in bow-tie nanoantennas forming the arrays. Experiments show that for polarization of the input light producing excitation of the plasmonic resonances in the bow-tie nanoantennas, the SHG signal is enhanced; this despite the fact that the linear absorption spectrum is not dependent on polarization. The results are confirmed by electrodynamic simulations which demonstrate that SHG is also determined by the local field distribution in the nanoarrays. Moreover, the maximum of SHG intensity is observed at slightly off-resonance excitation, as implemented in the experiments, showing a close relation between the polarization dependence and the structure of the material, additionally revealing the importance of the presence of non-normal electric field components as under focused beam and oblique illumination.

Relationship of GUN1 to FUG1 in chloroplast protein homeostasis

GUN1 integrates retrograde signals in chloroplasts but the underlying mechanism is elusive. FUG1, a chloroplast translation initiation factor, and GUN1 are co-expressed at the transcriptional level, and FUG1 co-immunoprecipitates with GUN1. We used mutants of GUN1 (gun1-103) and FUG1 (fug1-3) to analyse their functional relationship at the physiological and system-wide level, the latter including transcriptome and proteome analyses. Absence of GUN1 aggravates the effects of decreased FUG1 levels on chloroplast protein translation, resulting in transiently more pronounced phenotypes regarding photosynthesis, leaf colouration, growth and cold acclimation. The gun1-103 mutation also enhances variegation in the var2 mutant, increasing the fraction of white sectors, while fug1-3 suppresses the var2 phenotype. The transcriptomes of fug1-3 and gun1-103 plants are very similar, but absence of GUN1 alone has almost no effect on protein levels, whereas steady-state levels of chloroplast proteins are markedly decreased in fug1-3. In fug1 gun1 double mutants, effects on transcriptomes and particularly on proteomes are enhanced. Our results show that GUN1 function becomes critical when chloroplast proteostasis is perturbed by decreased rates of synthesis (fug1) or degradation (var2) of chloroplast proteins, or by low temperatures. The functions of FUG1 and GUN1 appear to be related, corroborating the view that GUN1 helps to maintain chloroplast protein homeostasis (proteostasis).

The causal role of the left parietal lobe in facilitation and inhibition of return

Following non-informative peripheral cues, responses are facilitated at the cued compared to the uncued location at short cue-target intervals. This effect reverses at longer intervals, giving rise to Inhibition of Return (IOR). The integration-segregation hypothesis (Lupiáñez, 2010) suggests that peripheral cues always produce an onset-detection cost regardless the behavioral cueing effect that is measured - either facilitation or IOR. In the present study, we used transcranial magnetic stimulation (TMS) to investigate the causal contribution of this detection cost to performance. We used a cueing paradigm with a target discrimination task that was preceded by a non-informative peripheral cue. The presence-absence of a central intervening event was manipulated. Online TMS to the left superior parietal lobe (compared to an active vertex stimulation) lead to an overall more positive effect (faster responses for cued as compared to uncued trials), by putatively impairing the detection cost contribution to performance. The data revealed a strong association between overall RT and the TMS effect, and also between overall RT and the integrity of the first branch of the left superior longitudinal fascicule. These results have critical implications not only for the open debate about the mechanism/s underlying spatial orienting effects, but also for the growing literature demonstrating that white matter connectivity is crucial for explaining inter-individual behavioral variability.

Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance

Chloroplast biogenesis is indispensable for proper plant development and environmental acclimation. In a screen for mutants affected in photosynthesis, we identified the protein phosphatase7-like (pp7l) mutant, which displayed delayed chloroplast development in cotyledons and young leaves. PP7L, PP7, and PP7-long constitute a subfamily of phosphoprotein phosphatases. PP7 is thought to transduce a blue-light signal perceived by crys and phy a that induces expression of SIGMA FACTOR5 (SIG5). We observed that, like PP7, PP7L was predominantly localized to the nucleus in Arabidopsis (Arabidopsis thaliana), and the pp7l phenotype was similar to that of the sig6 mutant. However, SIG6 expression was unaltered in pp7l mutants. Instead, loss of PP7L compromised translation and ribosomal RNA (rRNA) maturation in chloroplasts, pointing to a distinct mechanism influencing chloroplast development. Promoters of genes deregulated in pp7l-1 were enriched in PHYTOCHROME-INTERACTING FACTOR (PIF)-binding motifs and the transcriptome of pp7l-1 resembled those of pif and CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) signalosome complex (csn) mutants. However, pif and csn mutants, as well as cop1, cryptochromes (cry)1 cry2, and phytochromes (phy)A phyB mutants, do not share the pp7l photosynthesis phenotype. PhyB protein levels were elevated in pp7l mutants, but phyB overexpression plants did not resemble pp7l These results indicate that PP7L operates through a different pathway and that the control of greening and photosystem biogenesis can be separated. The lack of PP7L increased susceptibility to salt and high-light stress, whereas PP7L overexpression conferred resistance to high-light stress. Strikingly, PP7L was specifically recruited to Brassicales for the regulation of chloroplast development. This study adds another player involved in chloroplast biogenesis.

Nutraceutical Properties of Herbal Infusions from Six Native Plants of Argentine Patagonia

Six native plants of South America traditionally consumed in the Patagonian region (southern Argentina and Chile), namely: Adesmia boronioides Hook. f., Apium australe Thouars, Buddleja globosa Hope, Drimys andina (Reiche) R. Rodr. & Quezada, Dysphania multifida L. and Solidago chilensis Meyen were investigated to determine the nutraceutical properties of infusions of their aerial parts. The infusions were characterized in terms of their antioxidant activity, phenolic and flavonoid content, profile of phenolic compounds, general toxicity and cytotoxicity on two different human cell lines: T84 (derived from colon cancer) and HTR8/SVneo (not derived from cancer). Twenty-nine compounds, mainly phenolic acids and flavonoids, were identified. This is the first analysis of phenolic compounds in infusions from native plants of Patagonia. D. andina, B. globosa and S. chilensis showed high levels of antioxidants, even higher than those of Green Tea. The content of phenolic compounds correlated significantly with the antioxidant activity of the samples analyzed. The toxicity test indicated that the use of A. australe, B. globosa and D. multifida seems safe, but a moderate consumption is suggested for A. boronioides, D. andina and S. chilensis until more exhaustive and long-term results are available. Moreover, A. boronioides and S. chilensis showed anticancer potential due to their antiproliferative activity on human cancer cell lines.

Melanocyte development in the mouse tail epidermis requires the Adamts9 metalloproteinase

The mouse tail has an important role in the study of melanogenesis, because mouse tail skin can be used to model human skin pigmentation. To better understand the development of melanocytes in the mouse tail, we cloned two dominant ENU-generated mutations of the Adamts9 gene, Und3 and Und4, which cause an unpigmented ring of epidermis in the middle of the tail, but do not alter pigmentation in the rest of the mouse. Adamts9 encodes a widely expressed zinc metalloprotease with thrombospondin type 1 repeats with few known substrates. Melanocytes are lost in the Adamts9 mutant tail epidermis at a relatively late stage of development, around E18.5. Studies of our Adamts9 conditional allele suggest that there is a melanocyte cell-autonomous requirement for Adamts9. In addition, we used a proteomics approach, TAILS N-terminomics, to identify new Adamts9 candidate substrates in the extracellular matrix of the skin. The tail phenotype of Adamts9 mutants is strikingly similar to the unpigmented trunk belt in Adamts20 mutants, which suggests a particular requirement for Adamts family activity at certain positions along the anterior-posterior axis.

Preoperative Chemotherapy and Radiotherapy in the Management of Epidermoid Carcinoma of the Anal Canal

Sixteen patients affected by epidermoid carcinoma of the anal canal were treated preoperatively by means of an i.v. infusion of mitomycin C (15 mg/m2) on day 1 and 5-fluorouracil (750 mg/m2) days 1 to 5, followed by radiotherapy (3000 R in 3 weeks). Four to 6 weeks after the end of radiotherapy the response to the preoperative treatment was evaluated by means of biopsy. A reduction of the neoplastic mass was observed in 13 of the 16 patients. An evident correlation exists between the stage of the tumor and 1) the response to preoperative treatment, 2) local recurrence, and 3) long-term survival. In fact: 3/4 T1 patients reached a complete response (CR), and 1/4 T1, 5/5 T2 and 4/7 T3 patients achieved a partial response (PR); only 3/7 T3 patients never responded to preoperative treatment. After the initial surgery, only T2 (3/5) and T3 (4/7) patients underwent a second operation for a recurrence. Overall survival at 42 months was 62.5 % (T1, 100 %; T2, 80 %; T3, 28.5 2%).

The stress response of Ragusano donkey (Equus asinus) to different semen collection techniques

The aim of the present study was to characterize the stress response of donkeys to different semen collection techniques, comparing the physiological patterns of hormonal (adrenocorticotropic hormone: ACTH, cortisol) and biochemical variables (creatinine, total protein, urea, aspartate aminotransferase: AST, alanine aminotransferase: ALT), and routine seminal parameters and sexual behaviour. Twenty two healthy Ragusano donkeys were used and were randomly assigned to one of 2 groups based on different semen collection techniques. Group A was designated as the experimental group and included 16 donkeys submitted to semen collection by an artificial vagina (AV) "on the ground"; group B was designated as the control group, and included 6 donkeys submitted to semen collection by AV during the mount. The semen collection was performed in October, once a day for 10 consecutive days. Blood samples were collected in baseline conditions, before the onset of the treatments and within 30 min after, from the jugular vein of each subject. Two-way ANOVA showed a significant effect of semen collection technique and time points in group A for ACTH (p=0.0084), cortisol (p=0.0004) and creatinine (p=0.0131), with lower values after semen collection than before. A significant effect of semen collection technique and time points in group B for ACTH (p<0.0001) and cortisol (p<0.0001) was observed, with higher values after semen collection than before. The comparison between groups A and B values over different time points showed a significant effect after semen collection for ACTH (p<0.0001), cortisol (p<0.0001) and creatinine (p<0.0001), with the highest values in group B. This study provides the physiological evidence that semen collection on the ground in healthy donkeys could be used as an alternative strategy to induce a positive animal approach and economical advantages.

Metabolic control and complications in Italian people with diabetes treated with continuous subcutaneous insulin infusion

BACKGROUND AND AIM

The objective of this cross-sectional study was to evaluate the degree of glycaemic control and the frequency of diabetic complications in Italian people with diabetes who were treated with continuous subcutaneous insulin infusion (CSII).

METHODS AND RESULTS

Questionnaires investigating the organisation of diabetes care centres, individuals' clinical and metabolic features and pump technology and its management were sent to adult and paediatric diabetes centres that use CSII for treatment in Italy. Information on standard clinical variables, demographic data and acute and chronic diabetic complications was derived from local clinical management systems. The sample consisted of 6623 people with diabetes, which was obtained from 93 centres. Of them, 98.8% had type 1 diabetes mellitus, 57.2% were female, 64% used a conventional insulin pump and 36% used a sensor-augmented insulin pump. The median glycated haemoglobin (HbA_1c) level was 60 mmol/mol (7.6%). The HbA_1c target (i.e. <58 mmol/mol for age <18 years and <53 mmol/mol for age >18 years) was achieved in 43.4% of paediatric and 23% of adult participants. Factors such as advanced pump functions, higher rate of sensor use, pregnancy in the year before the study and longer duration of diabetes were associated with lower HbA_1c levels. The most common chronic complications occurring in diabetes were retinopathy, microalbuminuria and hypertension. In the year before the study, 5% of participants reported ≥1 episode of severe hypoglycaemic (SH) episodes (SH) and 2.6% reported ≥1 episode of ketoacidosis.

CONCLUSIONS

Advanced personal skills and use of sensor-based pump are associated with better metabolic control outcomes in Italian people with diabetes who were treated with CSII. The reduction in SH episodes confirms the positive effect of CSII on hypoglycaemia.

CLINICAL TRIAL REGISTRATION NUMBER

NCT 02620917 (ClinicalTrials.gov).

Skin complications of insulin injections: A case presentation and a possible explanation of hypoglycaemia

We are willing to report the case of a woman with type 2 diabetes treated with insulin, 4 shots a day, referring to us for 2 very large pigmented abdominal lipo-hypertrophy (LH) areas due to incorrect injection technique. The ultrasound examination showed the presence offluidwithin both LH lesions. Fluid examination showed insulin concentrations 13 times higher thancirculating ones. A12-month longstructured training on correct injection techniques normalized metabolic control and took rid of all sudden severe hypoglycemic episodes and the wide glycemic variability. In fact, both LH areas disappeared became softer and slightly smaller and got fluid-free. This is the first case documenting the presence of sort of an insulin reservoir within LH lesions and fluid reabsorption can explain the disappearance of hypoglycemic episodes and the improvement of glycemic control.

Penultimate deglacial warming across the Mediterranean Sea revealed by clumped isotopes in foraminifera

The variability of seawater temperature through time is a critical measure of climate change, yet its reconstruction remains problematic in many regions. Mg/Ca and oxygen isotope (δ¹⁸O_C) measurements in foraminiferal carbonate shells can be combined to reconstruct seawater temperature and δ¹⁸O (δ¹⁸O_SW). The latter is a measure of changes in local hydrology (e.g., precipitation/evaporation, freshwater inputs) and global ice volume. But diagenetic processes may affect foraminiferal Mg/Ca. This restricts its potential in many places, including the Mediterranean Sea, a strategic region for deciphering global climate and sea-level changes. High alkalinity/salinity conditions especially bias Mg/Ca temperatures in the eastern Mediterranean (eMed). Here we advance the understanding of both western Mediterranean (wMed) and eMed hydrographic variability through the penultimate glacial termination (TII) and last interglacial, by applying the clumped isotope (Δ₄₇) paleothermometer to planktic foraminifera with a novel data-processing approach. Results suggest that North Atlantic cooling during Heinrich stadial 11 (HS11) affected surface-water temperatures much more in the wMed (during winter/spring) than in the eMed (during summer). The method’s paired Δ₄₇ and δ¹⁸O_C data also portray δ¹⁸O_SW. These records reveal a clear HS11 freshwater signal, which attenuated toward the eMed, and also that last interglacial surface warming in the eMed was strongly amplified by water-column stratification during the deposition of the organic-rich (sapropel) interval known as S5.

Characterization and Evolution of the Cell Cycle-Associated Mob Domain-Containing Proteins in Eukaryotes

The MOB family includes a group of cell cycle-associated proteins highly conserved throughout eukaryotes, whose founding members are implicated in mitotic exit and co-ordination of cell cycle progression with cell polarity and morphogenesis. Here we report the characterization and evolution of the MOB domain-containing proteins as inferred from the 43 eukaryotic genomes so far sequenced. We show that genes for Mob-like proteins are present in at least 41 of these genomes, confirming the universal distribution of this protein family and suggesting its prominent biological function. The phylogenetic analysis reveals five distinct MOB domain classes, showing a progressive expansion of this family from unicellular to multicellular organisms, reaching the highest number in mammals. Plant Mob genes appear to have evolved from a single ancestor, most likely after the loss of one or more genes during the early stage of Viridiplantae evolutionary history. Three of the Mob classes are widespread among most of the analyzed organisms. The possible biological and molecular function of Mob proteins and their role in conserved signaling pathways related to cell proliferation, cell death and cell polarity are also presented and critically discussed.

The Human Odontoblast Cell Layer and Dental Pulp Proteomes and N-Terminomes

The proteome and N-terminome of the human odontoblast cell layer were identified for the first time by shotgun proteomic and terminal amine isotopic labeling of substrates (TAILS) N-terminomic analyses, respectively, and compared with that of human dental pulp stroma from 26 third molar teeth. After reverse-phase liquid chromatography-tandem mass spectrometry, >170,000 spectra from the shotgun and TAILS analyses were matched by 4 search engines to 4,888 and 12,063 peptides in the odontoblast cell layer and pulp stroma, respectively. Within these peptide groups, 1,543 and 5,841 protein N-termini, as well as 895 and 2,423 unique proteins, were identified with a false discovery rate of ≤1%. Thus, the human dental pulp proteome was expanded by 974 proteins not previously identified among the 4,123 proteins in our 2015 dental pulp study. Further, 222 proteins of the odontoblast cell layer were not found in the pulp stroma, suggesting many of these proteins are synthesized only by odontoblasts. When comparing the proteomes of older and younger donors, differences were more apparent in the odontoblast cell layer than in the dental pulp stroma. In the odontoblast cell layer proteome, we found proteomic evidence for dentin sialophosphoprotein, which is cleaved into dentin sialoprotein and dentin phosphoprotein. By exploring the proteome of the odontoblast cell layer and expanding the known dental pulp proteome, we found distinct proteome differences compared with each other and with dentin. Moreover, between 61% and 66% of proteins also occurred as proteoforms commencing with a neo-N-terminus not annotated in UniProt. Hence, TAILS increased proteome coverage and revealed considerable proteolytic processing, by identifying stable proteoforms in these dynamic dental tissues. All mass spectrometry raw data have been deposited to ProteomeXchange with the identifier <PXD006557>, with the accompanying metadata at Mendeley Data ( https://data.mendeley.com/datasets/b57zfh6wmy/1 ).

Long-term outcomes in ypT0 rectal cancers: An international multi-centric investigation on behalf of Italian Society of Surgical Oncology Young Board (YSICO)

AIM

To investigate the outcome and pattern of survivals of rectal cancer patients presenting a complete or nearly complete tumor response after neo-adjuvant treatment.

METHODS

Young surgeons <40 years old affiliated to the Italian Society of Surgical Oncology (YSICO) from 13 referral centers for colorectal cancer treatment, were invited to participate a retrospective study. Records from patients treated from 2005 to 2015 with a pathological diagnosis of ypT0/ypTis were retrieved and pooled in a common data-base for statistical purposes. All clinical and pathological variables were reviewed. Univariate and multivariate analyses were conducted with the end-point of survivals.

RESULTS

Two hundreds and sixty-one patients were analyzed including 237 ypT0 and 24 ypTis. Nodal positive patients were 8.7%. More than sixty-six percent of the patients did not perform adjuvant chemotherapy, with a statistical difference comparing N0 versus N+ patients (66.8% vs 40.9%, p 0.02). Mean follow-up was of 47.6 months. Twenty-two relapses were observed, 91.6% at a distant site. The mean time to recurrence was of 35.3 months. On univariate analysis, the use of adjuvant chemotherapy correlated with better OS exclusively in ypT0N + patients and not in ypT0N0. Univariate and multivariate analyses documented nodal positivity as the only prognostic factor correlated with a worse OS.

CONCLUSION

Recurrences were mostly diagnosed at a distant site and within the third year of follow-up. Nodal positivity was the only variable independently correlated with a worse OS. Univariate analysis documented a benefit for the use of adjuvant chemotherapy treatment exclusively in ypT0N + rectal cancers.

Bioimpedance analysis, metabolic effects and safety of the association Berberis aristata/Bilybum marianum: a 52-week double-blind, placebo-controlled study in obese patients with type 2 diabetes

Berberine, a quaternary isoquinoline alkaloid present in Berberis aristata, is well known in terms of cholesterol-lowering, hypoglycemic, and insulin sensitizing effects. Because of its low oral bioavailability, to improve intestinal absorption it has been recently combined with silymarin (Silybum marianum). The aim of our placebo controlled study was to evaluate the effects of its association with silymarin on abdominal fat in overweight/obese patients with type 2 diabetes mellitus (T2DM). To do so, 136 obese subjects with T2DM and metabolic syndrome were analyzed for fasting blood glucose and insulin, Insulin Resistance index according to the Homeostatic Model Assessment (HOMA-R), total, HDL and LDL cholesterol, triglycerides, uric acid, BMI, waist circumference, waist to hip ratio and underwent bioelectrical impedance to assess % of abdominal fat. All the above-mentioned parameters, as recorded at enrollment, after 6 months and at the end of the study, had significantly improved in the BBR-treated group in respect to baseline and to the control group. A validated national cardiovascular risk score also improved significantly after BBR treatment in respect to placebo. Our results point to a clinically significant effect in obese people with T2DM and metabolic syndrome. Moreover, for the first time, they provide evidence of a significant uric acid lowering activity as an additive beneficial effect of the association BBR + silymarin.

Controlling second-harmonic generation at the nanoscale with monolithic AlGaAs-on-AlOx antennas

We review recent achievements in the field of nanoscale nonlinear AlGaAs photonics based on all-dielectric optical antennas. After discussing the motivation and main technological challenges for the development of an AlGaAs monolithic platform for χ ⁽²⁾ nonlinear nanophotonics, we present numerical and experimental investigations of the second-order nonlinear response and physical reasons for high efficiency of second-order nonlinear interactions in the AlGaAs nano-antennas. In particular, we emphasize the role of the dipolar resonances at the fundamental frequency and the multipolar resonances at the second harmonic wavelength. We also discuss second-harmonic generation directionality and show possible strategies to engineer the radiation pattern of nonlinear antennas.

Giant endometrial cyst of the liver: a case report and review of the literature

Endometriosis is a benign condition described as the presence of endometrial- like tissue found outside the uterine cavity. Hepatic endometriosis is one of the rarest localization of extrapelvic endometriosis, only 22 cases have been reported in the literature. The preoperative diagnosis of hepatic endometriosis is rather difficult because in about the half of the patient affected they had no history of endometriosis. Moreover radiological images reveal no characteristic findings for hepatic endometriosis. It is often described as cystic mass with or without solid component, difficult to distinguish from hepatic abscess, hematoma, cystoadenoma or malignant neoplasia. We report a case of a 27-year-old female with a large cystic mass involving the left lobe of the liver. The patient underwent laparoscopic exploration and converted to laparotomy for resection of giant hepatic endometriosis.

TMS of supplementary motor area (SMA) facilitates mental rotation performance: Evidence for sequence processing in SMA

In the present study we applied online transcranial magnetic stimulation (TMS) bursts at 10Hz to the supplementary motor area (SMA) and primary motor cortex to test whether these regions are causally involved in mental rotation. Furthermore, in order to investigate what is the specific role played by SMA and primary motor cortex, two mental rotation tasks were used, which included pictures of hands and abstract objects, respectively. While primary motor cortex stimulation did not affect mental rotation performance, SMA stimulation improved the performance in the task with object stimuli, and only for the pairs of stimuli that had higher angular disparity between each other (i.e., 100° and 150°). The finding that the effect of SMA stimulation was modulated by the amount of spatial orientation information indicates that SMA is causally involved in the very act of mental rotation. More specifically, we propose that SMA mediates domain-general sequence processes, likely required to accumulate and integrate information that are, in this context, spatial. The possible physiological mechanisms underlying the facilitation of performance due to SMA stimulation are discussed.

Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14

The data described provide a comprehensive resource for the family-wide active site specificity portrayal of the human matrix metalloproteinase family. We used the high-throughput proteomic technique PICS (Proteomic Identification of protease Cleavage Sites) to comprehensively assay 9 different MMPs. We identified more than 4300 peptide cleavage sites, spanning both the prime and non-prime sides of the scissile peptide bond allowing detailed subsite cooperativity analysis. The proteomic cleavage data were expanded by kinetic analysis using a set of 6 quenched-fluorescent peptide substrates designed using these results. These datasets represent one of the largest specificity profiling efforts with subsequent structural follow up for any protease family and put the spotlight on the specificity similarities and differences of the MMP family. A detailed analysis of this data may be found in Eckhard et al. (2015) [1]. The raw mass spectrometry data and the corresponding metadata have been deposited in PRIDE/ProteomeXchange with the accession number PXD002265.

A proteomic approach for the rapid, multi-informative and reliable identification of blood

Blood evidence is frequently encountered at the scene of violent crimes and can provide valuable intelligence in the forensic investigation of serious offences.

TAILS N-terminomic and proteomic datasets of healthy human dental pulp

The Data described here provide the in depth proteomic assessment of the human dental pulp proteome and N-terminome (Eckhard et al., 2015) [1]. A total of 9 human dental pulps were processed and analyzed by the positional proteomics technique TAILS (Terminal Amine Isotopic Labeling of Substrates) N-terminomics. 38 liquid chromatography tandem mass spectrometry (LC-MS/MS) datasets were collected and analyzed using four database search engines in combination with statistical downstream evaluation, to yield the by far largest proteomic and N-terminomic dataset of any dental tissue to date. The raw mass spectrometry data and the corresponding metadata have been deposited in ProteomeXchange with the PXD identifier <PXD002264>; Supplementary Tables described in this article are available via Mendeley Data (10.17632/555j3kk4sw.1).

Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses

Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with leucine locked in S1'. Similar negative cooperativity between P3 proline and the novel preference for asparagine in P1 cements our conclusion that non-prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency. Thus, unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond.

Protein Termini and Their Modifications Revealed by Positional Proteomics

A myriad of co- and post-translational modifications occur at protein N- and C-termini, resulting in an extra layer of proteome complexity and an additional source of protein regulation. Here, we review N- and C-terminal modifications and the contemporary positional proteomics techniques used to isolate protein terminal peptides from complex protein mixtures and characterize their diversity and occurrence in biological systems. Furthermore, these degradomics strategies--often referred to as N- and C-terminomics--represent dedicated high-throughput techniques to study proteolysis in dynamic living systems. Over the past decade, terminomics studies have provided indispensable information on the functional states of individual proteins, cell types, tissues, and biological processes and delivered fundamental new data for the Human Proteome Project, including high confidence identifications of many so-called "missing proteins", which had not been identified by traditional proteomics analyses.