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Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues. There is a great need of developing highly sensitive mass spectrometry-based proteomics analysis for small cell populations. Here, the authors establish a robotically controlled chip-based nanodroplet processing platform and demonstrate its ability to profile the proteome from 10–100 mammalian cells.

The legendary river Saraswati of Indian mythology has often been hypothesized to be an ancient perennial channel of the seasonal river Ghaggar that flowed through the heartland of the Bronze Age Harappan civilization in north-western India. Despite the discovery of abundant settlements along a major paleo-channel of the Ghaggar, many believed that the Harappans depended solely on monsoonal rains, because no proof existed for the river’s uninterrupted flow during the zenith of the civilization. Here, we present unequivocal evidence for the Ghaggar’s perennial past by studying temporal changes of sediment provenance along a 300 km stretch of the river basin. This is achieved using 40 Ar/ 39 Ar ages of detrital muscovite and Sr-Nd isotopic ratios of siliciclastic sediment in fluvial sequences, dated by radiocarbon and luminescence methods. We establish that during 80-20 ka and 9-4.5 ka the river was perennial and was receiving sediments from the Higher and Lesser Himalayas. The latter phase can be attributed to the reactivation of the river by the distributaries of the Sutlej. This revived perennial condition of the Ghaggar, which can be correlated with the Saraswati, likely facilitated development of the early Harappan settlements along its banks. The timing of the eventual decline of the river, which led to the collapse of the civilization, approximately coincides with the commencement of the Meghalayan Stage.

Lithic assemblages from the archaeological site of Attirampakkam, India, document processes of transition from Acheulian to Middle Palaeolithic cultures and substantial behavioural changes around 385,000 years ago and thereafter. Out of Africa, into Asia When hominins—members of Homo erectus or similar—left Africa more than 1.7 million years ago, they carried their signature tool: the Acheulian hand axe. As skeletal material is extremely scarce, human evolution in Eurasia is often charted by changes in the tools used, notably the gradual shift from Acheulian technologies into cultures known as 'Middle Stone Age' in Africa or 'Middle Palaeolithic' elsewhere. The transition to the Middle Palaeolithic outside Europe and Africa is vital to our understanding of the lives of hominins in Eurasia, and especially the dispersal of anatomically modern humans out of Africa and their subsequent migrations. Only limited evidence has been recovered from India, but Shanti Pappu and colleagues present new data from the archaeological site of Attirampakkam in southern India. Dates from the site suggest that in India the Middle Palaeolithic began around 385,000 years ago, consistent with dates emerging from Europe and Africa, and show that the Middle Palaeolithic transition occurred here much earlier than suggested by conventional ideas regarding the spread of modern humans into southern Asia. Luminescence dating at the stratified prehistoric site of Attirampakkam, India, has shown that processes signifying the end of the Acheulian culture and the emergence of a Middle Palaeolithic culture occurred at 385 ± 64 thousand years ago (ka), much earlier than conventionally presumed for South Asia 1 . The Middle Palaeolithic continued at Attirampakkam until 172 ± 41 ka. Chronologies of Middle Palaeolithic technologies in regions distant from Africa and Europe are crucial for testing theories about the origins and early evolution of these cultures, and for understanding their association with modern humans or archaic hominins, their links with preceding Acheulian cultures and the spread of Levallois lithic technologies 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 . The geographic location of India and its rich Middle Palaeolithic record are ideally suited to addressing these issues, but progress has been limited by the paucity of excavated sites and hominin fossils as well as by geochronological constraints 1 , 8 . At Attirampakkam, the gradual disuse of bifaces, the predominance of small tools, the appearance of distinctive and diverse Levallois flake and point strategies, and the blade component all highlight a notable shift away from the preceding Acheulian large-flake technologies 9 . These findings document a process of substantial behavioural change that occurred in India at 385 ± 64 ka and establish its contemporaneity with similar processes recorded in Africa and Europe 2 , 3 , 4 , 5 , 6 , 7 , 8 , 10 , 11 , 12 , 13 . This suggests complex interactions between local developments and ongoing global transformations. Together, these observations call for a re-evaluation of models that restrict the origins of Indian Middle Palaeolithic culture to the incidence of modern human dispersals after approximately 125 ka 19 , 21 .

Sandstones of the Sanu Formation from Jaisalmer basin, western India were studied for major, trace and rare earth element (REE) geochemistry to deduce their paleo-weathering, tectonic setting, source rock characteristics and provenance. Geochemical results suggest that these sandstones can be classified into sub-arkose, which is supported by petrographic observations. The chemical index of alteration (CIA) values indicate intense chemical weathering. The major, trace and rare earth elements concentration pattern reveals that the sediments of the Sanu Formation were derived from silicic rock sources. The elemental discrimination diagrams specifically (Gd/Yb) N against Eu/Eu* suggest the Archean provenance as source possibly Aravallis for the studied samples.

Centrosome overduplication promotes mitotic abnormalities, invasion and tumorigenesis. Cells regulate the number of centrosomes by limiting centriole duplication to once per cell cycle. The orthogonal orientation between a mother and a daughter centriole, established at the time of centriole duplication, is thought to block further duplication of the mother centriole. Loss of orthogonal orientation (disengagement) between two centrioles during anaphase is considered a licensing event for the next round of centriole duplication. Disengagement requires the activity of Polo-like kinase 1 (Plk1), but how Plk1 drives this process is not clear. Here we employ correlative live/electron microscopy and demonstrate that Plk1 induces maturation and distancing of the daughter centriole, allowing reduplication of the mother centriole even if the original daughter centriole is still orthogonal to it. We find that mother centrioles can undergo reduplication when original daughter centrioles are only ∼80 nm apart, which is the distance centrioles normally reach during prophase. The orthogonal orientation between centrioles is thought to prevent their reduplication. Shukla et al. show that Polo-like kinase 1-dependent daughter centriole maturation, reflected in increasing inter-centriolar distance, allows centriole reduplication prior to loss of orthogonal orientation.

Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggest that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites. Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.

Informed-Proteomics, a software suite for top-down proteomics analysis, consists of a high-accuracy liquid chromatography–mass spectrometry feature-finding algorithm, an efficient database search tool, and an interactive results viewer. Top-down proteomics, the analysis of intact proteins in their endogenous form, preserves valuable information about post-translation modifications, isoforms and proteolytic processing. The quality of top-down liquid chromatography–tandem MS (LC-MS/MS) data sets is rapidly increasing on account of advances in instrumentation and sample-processing protocols. However, top-down mass spectra are substantially more complex than conventional bottom-up data. New algorithms and software tools for confident proteoform identification and quantification are needed. Here we present Informed-Proteomics, an open-source software suite for top-down proteomics analysis that consists of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results viewer. We compare our tool with several other popular tools using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.

Systems biology offers considerable promise in uncovering novel pathways by which viruses and other microbial pathogens interact with host signaling and expression networks to mediate disease severity. In this study, we have developed an unbiased modeling approach to identify new pathways and network connections mediating acute lung injury, using severe acute respiratory syndrome coronavirus (SARS-CoV) as a model pathogen. We utilized a time course of matched virologic, pathological, and transcriptomic data within a novel methodological framework that can detect pathway enrichment among key highly connected network genes. This unbiased approach produced a high-priority list of 4 genes in one pathway out of over 3,500 genes that were differentially expressed following SARS-CoV infection. With these data, we predicted that the urokinase and other wound repair pathways would regulate lethal versus sublethal disease following SARS-CoV infection in mice. We validated the importance of the urokinase pathway for SARS-CoV disease severity using genetically defined knockout mice, proteomic correlates of pathway activation, and pathological disease severity. The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such as SARS-CoV. IMPORTANCE Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and 2003, and infected patients developed an atypical pneumonia, acute lung injury (ALI), and acute respiratory distress syndrome (ARDS) leading to pulmonary fibrosis and death. We identified sets of differentially expressed genes that contribute to ALI and ARDS using lethal and sublethal SARS-CoV infection models. Mathematical prioritization of our gene sets identified the urokinase and extracellular matrix remodeling pathways as the most enriched pathways. By infecting Serpine1-knockout mice, we showed that the urokinase pathway had a significant effect on both lung pathology and overall SARS-CoV pathogenesis. These results demonstrate the effective use of unbiased modeling techniques for identification of high-priority host targets that regulate disease outcomes. Similar transcriptional signatures were noted in 1918 and 2009 H1N1 influenza virus-infected mice, suggesting a common, potentially treatable mechanism in development of virus-induced ALI. Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 and 2003, and infected patients developed an atypical pneumonia, acute lung injury (ALI), and acute respiratory distress syndrome (ARDS) leading to pulmonary fibrosis and death. We identified sets of differentially expressed genes that contribute to ALI and ARDS using lethal and sublethal SARS-CoV infection models. Mathematical prioritization of our gene sets identified the urokinase and extracellular matrix remodeling pathways as the most enriched pathways. By infecting Serpine1-knockout mice, we showed that the urokinase pathway had a significant effect on both lung pathology and overall SARS-CoV pathogenesis. These results demonstrate the effective use of unbiased modeling techniques for identification of high-priority host targets that regulate disease outcomes. Similar transcriptional signatures were noted in 1918 and 2009 H1N1 influenza virus-infected mice, suggesting a common, potentially treatable mechanism in development of virus-induced ALI.

The broad range and diversity of interferon-stimulated genes (ISGs) function to induce an antiviral state within the host, impeding viral pathogenesis. While successful respiratory viruses overcome individual ISG effectors, analysis of the global ISG response and subsequent viral antagonism has yet to be examined. Employing models of the human airway, transcriptomics and proteomics datasets were used to compare ISG response patterns following highly pathogenic H5N1 avian influenza (HPAI) A virus, 2009 pandemic H1N1, severe acute respiratory syndrome coronavirus (SARS-CoV), and Middle East respiratory syndrome CoV (MERS-CoV) infection. The results illustrated distinct approaches utilized by each virus to antagonize the global ISG response. In addition, the data revealed that highly virulent HPAI virus and MERS-CoV induce repressive histone modifications, which downregulate expression of ISG subsets. Notably, influenza A virus NS1 appears to play a central role in this histone-mediated downregulation in highly pathogenic influenza strains. Together, the work demonstrates the existence of unique and common viral strategies for controlling the global ISG response and provides a novel avenue for viral antagonism via altered histone modifications. IMPORTANCE This work combines systems biology and experimental validation to identify and confirm strategies used by viruses to control the immune response. Using a novel screening approach, specific comparison between highly pathogenic influenza viruses and coronaviruses revealed similarities and differences in strategies to control the interferon and innate immune response. These findings were subsequently confirmed and explored, revealing both a common pathway of antagonism via type I interferon (IFN) delay as well as a novel avenue for control by altered histone modification. Together, the data highlight how comparative systems biology analysis can be combined with experimental validation to derive novel insights into viral pathogenesis. This work combines systems biology and experimental validation to identify and confirm strategies used by viruses to control the immune response. Using a novel screening approach, specific comparison between highly pathogenic influenza viruses and coronaviruses revealed similarities and differences in strategies to control the interferon and innate immune response. These findings were subsequently confirmed and explored, revealing both a common pathway of antagonism via type I interferon (IFN) delay as well as a novel avenue for control by altered histone modification. Together, the data highlight how comparative systems biology analysis can be combined with experimental validation to derive novel insights into viral pathogenesis.

This paper presents an image enhancement technique based on super-resolution approach. The method uses fractional filters and reconstructs the output image by projection on convex sets (POCS) method. First, we generate a reference frame by using low-resolution frames and enhanced it by an adaptive fractional mask. Then the speed-up robust feature (SURF) is used to find the matching between low-resolution frames and the reference frame. Finally, the residuals between matching are reduced by the POCS reconstruction approach. To recover the high-frequency components, we have used a fractional integral mask in the POCS reconstruction process. We have compared the experimental results with some other existing methods from literature. Simulation results show that the proposed approach is efficient and returns a good quality image.