Miracle-dz/UniFAR-FTUs huggingface dataset:
Zirconium(IV)-IMAC for phosphopeptide enrichment in phosphoproteomics

Phosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics studies by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as Immobilized Metal ion Affinity Chromatography (IMAC) and Metal Oxide Affinity Chromatography (MOAC). We compared Zirconium (IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used Titanium (IV) IMAC (Ti-IMAC) and TiO2 magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior phosphopeptide sequencing and characterization by mass spectrometry (LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC, Ti-IMAC and TiO2 based workflows. The performance of Zr-IMAC was enhanced by 19-22% to recover up to 5173 phosphopeptides from 200 µg of protein extract from HepG2/C3A cells, making Zr-IMAC the preferred method for phosphopeptide enrichment in this study. Ti-IMAC and TiO2 performance were also optimized to improve phosphopeptide numbers by 28% and 35%, respectively. Furthermore, Zr-IMAC based phosphoproteomics in the magnetic microsphere format identified 23% more phosphopeptides than HPLC-based Fe(III)-IMAC for same sample amount (200 µg), thereby adding 37% more uniquely identified phosphopeptides. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this affinity enrichment method should be more widely used in biological and biomedical studies of cell signalling and in the search for disease-biomarkers.
Sequence Changes Modulate Peptoid Self-Association in Water

Peptoids, N-substituted glycine oligomers, are a class of diverse and sequence-specific peptidomimetics with wide-ranging applications. Advancing the functional repertoire of peptoids to emulate native peptide and protein functions requires engineering peptoids that adopt regular secondary and tertiary structures. An understanding of how changes to peptoid sequence change structural features, particularly in water-soluble systems, is underdeveloped. To address this knowledge gap, five 15-residue water-soluble peptoids that include naphthalene-functionalized side chains were designed, prepared, and subjected to a structural study using a palette of techniques. Peptoid sequence designs were based on a putative amphiphilic helix peptoid bearing structure-promoting (S)-N-(1-naphthylethyl)glycine residues whose self-association in water has been studied previously. New peptoid variants reported here include sequence changes that influenced peptoid conformational flexibility, functional group patterning (amphiphilicity), and hydrophobicity. Peptoid structures were evaluated and compared using circular dichroism spectroscopy, fluorescence spectroscopy, and size exclusion chromatography. Spectral data confirmed that sequence changes alter peptoids' degree of assembly and the organization of self-assembled structures in aqueous solutions. Insights gained in these studies will inform the design of new water-soluble peptoids with regular structural features, including desirable higher-order (tertiary and quaternary) structural features.
Microbial, Physical, and Chemical Changes in Galveston Bay Following an Extreme Flooding Event, Hurricane Harvey

Hurricane Harvey (category four storm) made landfall along the coast of Texas (United States) and then stalled out over Texas and Louisiana, releasing 1.29 × 1011 m3 of precipitation over 5 days. This caused extensive flooding that elevated freshwater river discharge and land runoff into Galveston Bay and eventually into the Gulf of Mexico. The floodwaters delivered a significant influx of dissolved organic carbon (DOC), organic pollutants and nutrients along with terrestrial and freshwater associated microbes. Over the 24 days following the flooding event, samples were collected on five cruises across Galveston Bay from the mouth of the San Jacinto River (Houston, TX, United States) to the Gulf of Mexico. Parameters measured for this study include: water quality (temperature, salinity, pH, and dissolved oxygen), nutrients (NO3–, NO2–, NH4+, Pi, and HSiO3–), polycyclic aromatic hydrocarbons (PAHs), pharmaceuticals (cotinine, carbamazepine, carbamazepine-epoxide, and prednisone), biocide (imidacloprid), DOC, bacteria, and the eukaryotic community composition (16S and 18S rRNA genes). In the week after the flood event, bay-wide salinities decreased to 0–5 compared to the higher pre-Harvey salinities of 20–30 (recorded 5 days before the flood). Water treatment facilities and petrochemical plants were compromised due to the heavy flooding in the region. Increased concentrations of DOC, nutrients, PAHs, pharmaceuticals, and biocides were observed across Galveston Bay immediately following the storm. During the 4 weeks after Harvey, concentrations of DOC, nutrients, and organic pollutants began to decrease coinciding with rising salinities as the freshwater was flushed into the Gulf of Mexico and seawater began moving back into the Bay. Successive blooms of Chlorophyta, diatoms (Bacillariophyta), and dinoflagellates (Dinophyta) occurred similar to post-storm communities from past hurricanes that have impacted estuarine systems along the Gulf of Mexico. The bacterial community showed an increase in the abundance of bacteria associated with terrestrial soils and freshwater at the initial time point and then decreased over time and were replaced by their estuarine and marine relatives within the month following the hurricane. The eukaryotic community changed substantially following Harvey and did not recover to pre-Harvey conditions during our study period, suggesting a longer recovery time compared to the prokaryotes. Although the water quality parameters and prokaryotic community showed signs of returning to pre-Harvey conditions within the month following the flood event, long-term impacts need to be measured in the years following the flood.
Mapping the genetic and environmental aetiology of autistic traits in Sweden and the United Kingdom

Background Autistic traits are influenced by both genetic and environmental factors, and are known to vary geographically in prevalence. But to what extent does their aetiology also vary from place to place? Methods We applied a novel spatial approach to data on autistic traits from two large twin studies, the Child and Adolescent Twin Study in Sweden (CATSS; N=16,677, including 8,307 twin pairs) and the Twins Early Development Study in the UK (TEDS; N=11,594, including 5,796 twin pairs), to explore how the influence of nature and nurture on autistic traits varies from place to place. Results We present maps of gene- and environment-by geography interactions in Sweden and the United Kingdom (UK), showing geographical variation in both genetic and environmental influences across the two countries. In Sweden genetic influences appear higher in the far south and in a band running across the centre of the country. Environmental influences appear greatest in the south and north, with reduced environmental influence across the central band. In the UK genetic influences appear greater in the south, particularly in more central southern areas and the southeast, the Midlands and the north of England. Environmental influences appear greatest in the south and east of the UK, with less influence in the north and the west. Conclusions We hope this systematic approach to identifying aetiological interactions will inspire research to examine a wider range of previously unknown environmental influences on the aetiology of autistic traits. By doing so, we will gain greater understanding of how these environments draw out or mask genetic predisposition and interact with other environmental influences in the development of autistic traits.
Plasma-derived exosome-like vesicles are enriched in lyso-phospholipids and pass the blood-brain barrier

Exosomes are vesicles involved in intercellular communication. Their membrane structure and core content is largely dependent on the cell of origin. Exosomes have been investigated both for their biological roles and their possible use as disease biomarkers and drug carriers. These potential technological applications require the rigorous characterization of exosomal blood brain barrier permeability and a description of their lipid bilayer composition. To achieve these goals, we have established a 3D static blood brain barrier system based on existing systems for liposomes and a complementary LC-MS/MS and 31P nuclear magnetic resonance methodology for the analysis of purified human plasma-derived exosome-like vesicles. Results show that the isolated vesicles pass the blood brain barrier and are taken up in endothelial cells. The compositional analysis revealed that the isolated vesicles are enriched in lyso phospholipids and do not contain phosphatidylserine. These findings deviate significantly from the composition of exosomes originating from cell culture, and may reflect active removal by macrophages that respond to exposed phosphahtidylserine.
Oleic acid Induces Tissue Resident FoxP3 Regulatory T cell Lineage Stability and Suppressive Functions

FoxP3 positive regulatory T cells (Tregs) rely on fatty acid β-oxidation (FAO)-driven OXPHOS for differentiation and function. Recent data have demonstrated a role for Tregs in the maintenance of tissue homeostasis with tissue-resident Tregs possessing tissue-specific transcriptomes. However, specific signals that establish these tissue-resident Tregs programs are largely unknown. As Tregs metabolically rely on FAO, and considering the lipid-rich environments of tissues, we hypothesized that environmental lipids drive Treg homeostasis. Using human adipose tissue as a model for tissue residency, we identify oleic acid as the most prevalent free fatty acid in human adipose tissue. Mechanistically, oleic acid amplifies Treg FAO-driven OXPHOS metabolism, creating a positive feedback mechanism that induces the expression of Foxp3 and enhances phosphorylation of STAT5, which acts to stabilize the Treg lineage and increase suppressive function. Comparing the transcriptomic program induced by oleic acid to that of the pro-inflammatory arachidonic acid, we find that Tregs sorted from peripheral blood and adipose of healthy donors transcriptomically resemble the oleic acid in vitro treated Tregs, whereas Tregs obtained from the adipose tissue of relapsing-remitting MS patients more closely resemble an arachidonic acid profile. Finally, we find that oleic acid concentrations are reduced in the fat tissue of MS patients, and exposure of dysfunctional MS Tregs to oleic acid restores defects in their suppressive function. These data demonstrate the importance of fatty acids in regulating tissue inflammatory signals.
Spatio-temporal mapping of mechanical force generated by macrophages during FcγR-dependent phagocytosis reveals adaptation to target stiffness

Macrophage phagocytosis is a strikingly flexible process central to pathogen clearance and is an attractive target for the development of anti-cancer immunotherapies. To harness the adaptability of phagocytosis, we must understand how macrophages can successfully deform their plasma membrane. While the signaling pathways and the molecular motors responsible for this deformation have been studied for many years, we only have limited insight into the mechanics that drive the formation of the phagocytic cup. Using Traction Force Microscopy (TFM), we have been able to characterize the spatio-temporal dynamics of mechanical forces generated in the course of FcγR-dependent frustrated phagocytosis and we determined whether this was affected by the stiffness of the potential phagocytic targets. We observed that frustrated phagocytosis is an atypical form of spreading where the cell deformation rate is unaffected by the substrate stiffness. Interestingly, the cell initially extends without forces being recorded then switches to a mode of pseudopod extension involving spatially organized force transmission. Importantly we demonstrate that macrophages adapt to the substrate stiffness primarily through a modulation of the magnitude of mechanical stress exerted, and not through modification of the mechanical stress kinetics or distribution. Altogether, we suggest that macrophage phagocytosis exhibits a clear resilience to variations of the phagocytic target stiffness and this is favored by an adaptation of their mechanical response.
The Malnutritional Status of the Host as a Virulence Factor for New Coronavirus SARS-CoV-2

1 IRCCS Orthopedic Institute Galeazzi, Scientific Direction, Milan, Italy, Health Management, IRCCS Orthopedic Institute Galeazzi, Milan, Italy, Department of Biomedical Sciences for Health, University of Milan, Milan, Italy, 4 Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Orthopedic Institute Galeazzi, Milan, Italy, Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland, 6 Post-operative Intensive Care Unit & Anesthesia, IRCCS Orthopedic Institute Galeazzi, Milan, Italy, 7 Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
A Retrospective Exploration of Targeted Maintenance Therapy in Advanced Colorectal Cancer: Based on the Background of Chinese Patient Assistance Program

Background: Maintenance therapy with bevacizumab (Bev) in patients with colorectal cancer (CRC) provides progression-free survival (PFS) benefits. However, the role of maintenance therapy with an anti-EGFR monoclonal antibody has not been established. Methods: Eligible CRC patients were assigned to maintenance therapy with cetuximab (Cet; Cet group) or Bev (Bev group). PFS, the duration of maintenance therapy, and safety were analyzed. Cox multivariate regression analyses were performed to determine independent prognostic factors. Results: A total of 143 eligible patients were assigned to the Cet (n = 79) or Bev (n = 64) groups. In the Cet group, all patients had KRAS wild-type. The baseline characteristics were well-balanced between the two groups, except for a higher percentage of patients with a left-sided primary tumor in the Cet group than in the Bev group (86.1 vs. 62.5%, P < 0.0001). The median PFS was not significantly different between the Cet group and the Bev group: 5.9 months (95% CI 2.30–9.50) vs. 7.0 months (95% CI 3.69–10.31) (HR 1.17, 95% CI 0.77–1.79, P = 0.45). The median duration of maintenance therapy in the Cet group was shorter than that in the Bev group: 4.0 months (95% CI 1.94–5.99) vs. 4.8 months (95% CI 2.68–6.98) (HR 0.90, 95% CI 0.61–1.33; P = 0.59). The subgroup analyses showed that the median PFS for the first maintenance therapy and the second maintenance therapy were 3.2 months (95% CI 1.69–4.78) and 5.2 months (95% CI 1.58–8.83), respectively (HR 0.89, 95% CI 0.44–1.81; P = 0.75). Conclusions: This study suggests that maintenance therapy with Cet or Bev can be considered an appropriate option following induction chemotherapy for selected patients with advanced CRC. Multiple maintenance therapy seems to confer survival benefits in advanced CRC. Maintenance therapy with Cet after first-line induction chemotherapy seems to be associated with greater survival benefits.
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

Influenza virus infections are major causes of morbidity and mortality. Research using cultured cells, bulk tissue, and animal models cannot fully capture human disease dynamics. Many aspects of virus-host interactions in a natural setting remain unclear, including the specific cell types that are infected and how they and neighboring bystander cells contribute to the overall antiviral response. To address these questions, we performed single-cell RNA sequencing (scRNA-Seq) on cells from freshly collected nasal washes from healthy human donors and donors diagnosed with acute influenza during the 2017-18 season. We describe a previously uncharacterized goblet cell population, specific to infected individuals, with high expression of MHC class II genes. Furthermore, leveraging scRNA-Seq reads, we obtained deep viral genome coverage and developed a model to rigorously identify infected cells that detected influenza infection in all epithelial cell types and even some immune cells. Our data revealed that each donor was infected by a unique influenza variant and that each variant was separated by at least one unique non-synonymous difference. Our results demonstrate the power of massively-parallel scRNA-Seq to study viral variation, as well as host and viral transcriptional activity during human infection.
Cold acclimation has a differential effect on leaf vascular bundle structure and carbon export rates in natural Arabidopsis accessions originating from southern and northern Europe

Acclimation to low but non-freezing temperature represents an ecologically important process for Arabidopsis thaliana but also for many other plant species from temperate regions. Cold acclimation comprises and affects numerous molecular and physiological processes and the maintenance of sugar supply of sink tissue by photosynthetically active source tissue is preliminary for plant survival. Here, we analysed the correlation of changes in vascular bundle structure at the leaf petiole and sucrose exudation rates before and after cold acclimation. We compared six natural Arabidopsis accessions originating from southern and northern Europe. Photosynthetic capacities, i.e. maximum and effective quantum yield of photosystem II, revealed a significant effect of condition but not of genotype. Only for northern accessions we observed a highly significant negative correlation between leaf sucrose exudation rates, xylem and petiole cross section areas. Further, only for northern accessions we observed a significant increase of vascular bundle and leaf petiole cross section area during cold acclimation. In contrast, variance of cross section areas of cold acclimated southern accessions was strongly reduced compared to control plants while mean areas remained similar under both conditions. In summary, our findings suggest that natural Arabidopsis accessions from northern Europe significantly adjust sink strength and leaf vascular bundle structure to stabilize plant growth and photosynthesis for survival under low and freezing temperature.
Synaptic learning rules for sequence learning

Remembering the temporal order of a sequence of events is a task easily performed by humans in everyday life, but the underlying neuronal mechanisms are unclear. This problem is particularly intriguing as human behavior often proceeds on a time scale of seconds, which is in stark contrast to the much faster millisecond time-scale of neuronal processing in our brains. One long-held hypothesis in sequence learning suggests that a particular temporal fine-structure of neuronal activity — termed “phase precession” — enables the compression of slow behavioral sequences down to the fast time scale of the induction of synaptic plasticity. Using mathematical analysis and computer simulations, we find that — for short enough synaptic learning windows — phase precession can improve temporal-order learning tremendously and that the asymmetric part of the synaptic learning window is essential for temporal-order learning. To test these predictions, we suggest experiments that selectively alter phase precession or the learning window and evaluate memory of temporal order.
The folding and unfolding behavior of ribonuclease H on the ribosome

The health of a cell depends on accurate translation and proper protein folding, whereas misfolding can lead to aggregation and disease. The first opportunity for a protein to fold occurs during translation, when the ribosome and surrounding environment can affect the nascent chain energy landscape. However, quantifying these environmental effects is challenging because ribosomal proteins and rRNA preclude most spectroscopic measurements of protein energetics. Here, we have applied two gel-based approaches, pulse proteolysis and force-profile analysis, to probe the folding and unfolding pathways of RNase H (RNH) nascent chains stalled on the prokaryotic ribosome in vitro. We found that ribosome-stalled RNH has an increased unfolding rate compared with free RNH. Because protein stability is related to the ratio of the unfolding and folding rates, this increase completely accounts for the observed change in protein stability and indicates that the folding rate is unchanged. Using arrest peptide–based force-profile analysis, we assayed the force generated during the folding of RNH on the ribosome. Surprisingly, we found that population of the RNH folding intermediate is required to generate sufficient force to release a stall induced by the SecM stalling sequence and that readthrough of SecM directly correlates with the stability of the RNH folding intermediate. Together, these results imply that the folding pathway of RNH is unchanged on the ribosome. Furthermore, our findings indicate that the ribosome promotes RNH unfolding while the nascent chain is proximal to the ribosome, which may limit the deleterious effects of RNH misfolding and assist in folding fidelity.
Selective enhancement of low-gamma activity by tACS improves phonemic processing and reading accuracy in dyslexia

The phonological deficit in dyslexia is associated with altered low-gamma oscillatory function in left auditory cortex, but a causal relationship between oscillatory function and phonemic processing has never been established. After confirming a deficit at 30 Hz with electroencephalography (EEG), we applied 20 minutes of transcranial alternating current stimulation (tACS) to transiently restore this activity in adults with dyslexia. The intervention significantly improved phonological processing and reading accuracy as measured immediately after tACS. The effect was selective to 30 Hz stimulation, and proportional to dyslexia severity. Importantly, we observed that the focal intervention on the left auditory cortex also decreased 30 Hz activity in the right superior temporal cortex, resulting in reinstating a left dominance for the oscillatory response, as present in controls. These findings formally establish a causal role of neural oscillations in phonological processing, and offer solid neurophysiological grounds for a potential correction of low-gamma anomalies, and for alleviating of the phonological deficit in dyslexia.
Microbial communities in an ultra-oligotrophic sea are more affected by season than by distance from shore

Marine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. We studied temporal and spatial patterns of the microbial community structure and activity along a coast to offshore transect from the Israeli coast of the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of two consecutive years. The ultra-oligotrophic status of the South Eastern Mediterranean Sea was reflected in the microbial community composition that was dominated by oligotrophic microbial groups such as SAR11 throughout the year, even at the most coastal station sampled. Seasons affected microbial communities much more than distance from shore explaining about half of the observed variability in the microbial community, compared to only about 6% that was explained by station. However, the most coastal site differed significantly in community structure and activity from the three further offshore stations in early winter and summer, but not in spring. Our data on the microbial community composition and its seasonality from a transect into the South Eastern Levantine basin support the notion that the EMS behaves similar to open gyres rather than an inland sea.