DESP demixes cell-state profiles from dynamic bulk molecular measurements

Understanding the dynamic expression of proteins and other key molecules driving phenotypic remodeling in development and pathobiology has garnered widespread interest, yet the exploration of these systems at the foundational resolution of the underlying cell states has been significantly limited by technical constraints. Here, we present DESP, an algorithm designed to leverage independent estimates of cell-state proportions, such as from single-cell RNA sequencing, to resolve the relative contributions of cell states to bulk molecular measurements, most notably quantitative proteomics, recorded in parallel. We applied DESP to an in vitro model of the epithelial-to-mesenchymal transition and demonstrated its ability to accurately reconstruct cell-state signatures from bulk-level measurements of both the proteome and transcriptome, providing insights into transient regulatory mechanisms. DESP provides a generalizable computational framework for modeling the relationship between bulk and single-cell molecular measurements, enabling the study of proteomes and other molecular profiles at the cell-state level using established bulk-level workflows.

The Outcome of Treatment in Second Branchial Cleft Anomalies: A Case Series

Background Branchial-cleft anomalies are second only to thyroglossal duct anomalies among congenital malformations of the neck, and second branchial-cleft anomalies are the most common. These include branchial cysts, branchial sinuses, and branchial fistulas. Clinical symptoms include neck swelling and a discharging sinus or fistula opening. In a small number of cases, they can lead to major complications like abscesses or malignant changes. Surgical resection is the treatment of choice. Various approaches to resection and sclerotherapy have been tried. In this study, we present our treatment outcome with branchial cleft anomalies at a rural tertiary medical care hospital. Objectives To document the various presentations, clinical features, and outcomes of treatment with second branchial cleft anomalies. Methods This retrospective observational study included 16 patients operated on for second branchial-cleft anomalies. A detailed medical history was elicited, and an accurate clinical examination was done. A contrast-enhanced computed tomography (CECT) scan was done in all cases. A few cases required a fistulogram. The cysts, sinuses, or fistulas were resected en bloc by a single neck crease incision. Primary closure was done in all cases. A recurrence or pharyngocutaneous fistula required axial flap reconstruction. The complications and recurrences were documented. Result There were six children and 10 adults in our study. Seven cysts, five sinuses, and four fistulas were present, of which four were iatrogenic. In seven patients, imaging could not show the entire tract. There were four fistulas from the oropharynx to a cutaneous opening in the neck. A complete resection was done for all. Two pharyngocutaneous fistulas were treated with a pectoralis major myocutaneous (PMMC) flap. Three patients had wound dehiscence postoperatively. None of the patients had neurological or vascular injuries. Conclusion Second branchial cleft anomalies can be completely excised by a single neck crease incision. Meticulous surgery results in a low recurrence or complication rate. Following complete excision, in type IV anomalies, a purse-string suture at the pharyngeal opening ensures good closure and no recurrences.

Comparison Between Clinical Outcome of Intralesional Human Placental Extract Alone and Topical Application of Placental Extract Gel After Fibrotomy in Oral Submucous Fibrosis

BACKGROUND

Oral submucous fibrosis (OSMF) is a premalignant condition prevalent in our country. Juxtaepithelial inflammation with progressive hyalinization of the lamina propria results in stiffness and fibrosis of the oral mucosa, characterised by trismus, ankyloglossia, and a burning sensation. Various methods of treatment have been tried in these cases, which include placental extract injections and the cutting of fibrous bands. In this study, we aim to compare the outcome of intra-lesional placental extract injection with fibrotomy and placental extract gel application in OSMF.

METHODOLOGY

This prospective interventional study included 58 patients clinically diagnosed with OSMF grades II and III at a rural tertiary care hospital between January 2021 and August 2022. The patients were randomised into two groups: group I received 1 ml of intra-lesional human placental extract injection in the submucosal plane of the buccal mucosa and retro-molar trigone (RMT) once a week for five consecutive weeks, and group II was subjected to a transverse division of fibrotic bands in the submucosal plane under general anaesthesia. The surgical wound was left open, and swabs soaked in human-purified placental extract gel were placed in the wound for two hours twice daily until the surgical wound was epithelialized and healed. The patients in both groups I and II were advised to do jaw opening exercises, and weekly follow-up was done. Findings with regard to maximum mouth opening, colour of mucosa, and burning sensation in the oral cavity based on a Likert scale were documented. At the end of five months, the pre-treatment and post-treatment results documented were compared.

RESULTS

All patients were between 20 and 60 years of age and were addicted to chewing areca nuts with tobacco. Bilateral involvement was present in all patients, with extension into the RMT and soft palate seen in 31%. Improvement in mouth opening was between 4 mm and 6 mm in group II, and relief of burning sensation and mucosal colour was better in group I.

CONCLUSION

Intra-lesional placental extract injections help in the improvement of the mucosa and relief from the burning sensation. Fibrotomy with placental extract gel application is better at relieving trismus in OSMF. Aggressive mouth-opening exercises may improve mouth opening following the above procedures.

Prethermal Fragmentation in a Periodically Driven Fermionic Chain

We study a fermionic chain with nearest-neighbor hopping and density-density interactions, where the nearest-neighbor interaction term is driven periodically. We show that such a driven chain exhibits prethermal strong Hilbert space fragmentation (HSF) in the high drive amplitude regime at specific drive frequencies ω_{m}^{*}. This constitutes the first realization of HSF for out-of-equilibrium systems. We obtain analytic expressions of ω_{m}^{*} using a Floquet perturbation theory and provide exact numerical computation of entanglement entropy, equal-time correlation functions, and the density autocorrelation of fermions for finite chains. All of these quantities indicate clear signatures of strong HSF. We study the fate of the HSF as one tunes away from ω_{m}^{*} and discuss the extent of the prethermal regime as a function of the drive amplitude.

Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT

A proper understanding of disease etiology will require longitudinal systems-scale reconstruction of the multitiered architecture of eukaryotic signaling. Here we combine state-of-the-art data acquisition platforms and bioinformatics tools to devise PAMAF, a workflow that simultaneously examines twelve omics modalities, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. We apply PAMAF in an established in vitro model of TGFβ-induced epithelial to mesenchymal transition (EMT) to quantify >61,000 molecules from 12 omics and 10 timepoints over 12 days. Bioinformatics analysis of this EMT-ExMap resource allowed us to identify; -topological coupling between omics, -four distinct cell states during EMT, -omics-specific kinetic paths, -stage-specific multi-omics characteristics, -distinct regulatory classes of genes, -ligand-receptor mediated intercellular crosstalk by integrating scRNAseq and subcellular proteomics, and -combinatorial drug targets (e.g., Hedgehog signaling and CAMK-II) to inhibit EMT, which we validate using a 3D mammary duct-on-a-chip platform. Overall, this study provides a resource on TGFβ signaling and EMT.

GPS2-mediated regulation of the adipocyte secretome modulates adipose tissue remodeling at the onset of diet-induced obesity

OBJECTIVE

Dysfunctional, unhealthy expansion of white adipose tissue due to excess dietary intake is a process at the root of obesity and Type 2 Diabetes development. The objective of this study is to contribute to a better understanding of the underlying mechanism(s) regulating the early stages of adipose tissue expansion and adaptation to dietary stress due to an acute, high-fat diet (HFD) challenge, with a focus on the communication between adipocytes and other stromal cells.

METHODS

We profiled the early response to high-fat diet exposure in wildtype and adipocyte-specific GPS2-KO (GPS2-AKO) mice at the cellular, tissue and organismal level. A multi-pronged approach was employed to disentangle the complex cellular interactions dictating tissue remodeling, via single-cell RNA sequencing and FACS profiling of the stromal fraction, and semi-quantitative proteomics of the adipocyte-derived exosomal cargo after 5 weeks of HFD feeding.

RESULTS

Our results indicate that loss of GPS2 in mature adipocytes leads to impaired adaptation to the metabolic stress imposed by HFD feeding. GPS2-AKO mice are significantly more inflamed, insulin resistant, and obese, compared to the WT counterparts. At the cellular level, lack of GPS2 in adipocytes impacts upon other stromal populations, with both the eWAT and scWAT depots exhibiting changes in the immune and non-immune compartments that contribute to an increase in inflammatory and anti-adipogenic cell types. Our studies also revealed that adipocyte to stromal cell communication is facilitated by exosomes, and that transcriptional rewiring of the exosomal cargo is crucial for tissue remodeling. Loss of GPS2 results in increased expression of secreted factors promoting a TGFβ-driven fibrotic microenvironment favoring unhealthy tissue remodeling and expansion.

CONCLUSIONS

Adipocytes serve as an intercellular signaling hub, communicating with the stromal compartment via paracrine signaling. Our study highlights the importance of proper regulation of the 'secretome' released by energetically stressed adipocytes at the onset of obesity. Altered transcriptional regulation of factors secreted via adipocyte-derived exosomes (AdExos), in the absence of GPS2, contributes to the establishment of an anti-adipogenic, pro-fibrotic adipose tissue environment, and to hastened progression towards a metabolically dysfunctional phenotype.

Nematic-Fluctuation-Mediated Superconductivity Revealed by Anisotropic Strain in Ba(Fe_{1-x}Co_{x})_{2}As_{2}

Anisotropic strain is an external field capable of selectively addressing the role of nematic fluctuations in promoting superconductivity. We demonstrate this using polarization-resolved elasto-Raman scattering by probing the evolution of nematic fluctuations under strain in the normal and superconducting state of the paradigmatic iron-based superconductor Ba(Fe_{1-x}Co_{x})_{2}As_{2}. In the parent compound BaFe_{2}As_{2} we observe a strain-induced suppression of the nematic susceptibility which follows the expected behavior of an Ising order parameter under a symmetry breaking field. For the superconducting compound, the suppression of the nematic susceptibility correlates with the decrease of the critical temperature T_{c}, indicating a significant contribution of nematic fluctuations to electron pairing. Our results validate theoretical scenarios of enhanced T_{c} near a nematic quantum critical point.

Imaging the future: the emerging era of single-cell spatial proteomics

The proteome of a human cell is partitioned within organelles, such as the nucleus, and other subcellular compartments, such as the cytoplasm, forming a myriad of membrane-bound and membrane-free ultrastructures. This compartmentalization allows discrete biochemical processes to occur efficiently in isolation, with relevant proteins localized to appropriate niches to fulfill their biological function(s). Proper delivery and dynamic exchange of proteins between compartments underlie the regulation of many cellular processes, such as cell signaling, division, and programmed cell death. To this end, cells deploy dedicated trafficking mechanisms to ensure correct protein localization, as mis-localization can result in pathology. In addition to trafficking, variation in the expression, modification, and physical associations of proteins within and between cells can result in biological heterogeneity, motivating the need for single-cell measurements. In this review, we introduce diverse platform technologies developed for subcellular proteomics and high-throughput systems biology, with the aim of providing mechanistic insights into fundamental cell biological processes underlying healthy and diseased states, and valuable public data resources. In contrast to the rapidly advancing field of single-cell genomics, the single-cell spatial proteomics toolbox remains in its infancy, but is poised to make considerable advances in the coming years.

Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2

Human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative pathogen of the COVID-19 pandemic, exerts a massive health and socioeconomic crisis. The virus infects alveolar epithelial type 2 cells (AT2s), leading to lung injury and impaired gas exchange, but the mechanisms driving infection and pathology are unclear. We performed a quantitative phosphoproteomic survey of induced pluripotent stem cell-derived AT2s (iAT2s) infected with SARS-CoV-2 at air-liquid interface (ALI). Time course analysis revealed rapid remodeling of diverse host systems, including signaling, RNA processing, translation, metabolism, nuclear integrity, protein trafficking, and cytoskeletal-microtubule organization, leading to cell cycle arrest, genotoxic stress, and innate immunity. Comparison to analogous data from transformed cell lines revealed respiratory-specific processes hijacked by SARS-CoV-2, highlighting potential novel therapeutic avenues that were validated by a high hit rate in a targeted small molecule screen in our iAT2 ALI system.

PDX-derived organoids model in vivo drug response and secrete biomarkers

Patient-derived organoid models are proving to be a powerful platform for both basic and translational studies. Here we conduct a methodical analysis of pancreatic ductal adenocarcinoma (PDAC) tumor organoid drug response in paired patient-derived xenograft (PDX) and PDX-derived organoid (PXO) models grown under WNT-free culture conditions. We report a specific relationship between area under the curve value of organoid drug dose response and in vivo tumor growth, irrespective of the drug treatment. In addition, we analyzed the glycome of PDX and PXO models and demonstrate that PXOs recapitulate the in vivo glycan landscape. In addition, we identify a core set of 57 N-glycans detected in all 10 models that represent 50%-94% of the relative abundance of all N-glycans detected in each of the models. Last, we developed a secreted biomarker discovery pipeline using media supernatant of organoid cultures and identified potentially new extracellular vesicle (EV) protein markers. We validated our findings using plasma samples from patients with PDAC, benign gastrointestinal diseases, and chronic pancreatitis and discovered that 4 EV proteins are potential circulating biomarkers for PDAC. Thus, we demonstrate the utility of organoid cultures to not only model in vivo drug responses but also serve as a powerful platform for discovering clinically actionable serologic biomarkers.

Nematic fluctuations in the cuprate superconductor Bi2Sr2CaCu2O8+δ

Establishing the presence and the nature of a quantum critical point in their phase diagram is a central enigma of the high-temperature superconducting cuprates. It could explain their pseudogap and strange metal phases, and ultimately their high superconducting temperatures. Yet, while solid evidences exist in several unconventional superconductors of ubiquitous critical fluctuations associated to a quantum critical point, in the cuprates they remain undetected until now. Here using symmetry-resolved electronic Raman scattering in the cuprate \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{Bi}}_2{\mathrm{Sr}}_2{\mathrm{CaCu}}_2{\mathrm{O}}_{8+\delta}$$\end{document}Bi2Sr2CaCu2O8+δ, we report the observation of enhanced electronic nematic fluctuations near the endpoint of the pseudogap phase. While our data hint at the possible presence of an incipient nematic quantum critical point, the doping dependence of the nematic fluctuations deviates significantly from a canonical quantum critical scenario. The observed nematic instability rather appears to be tied to the presence of a van Hove singularity in the band structure.

Solid evidence of quantum fluctuations associated to a quantum critical point in cuprate superconductors remains elusive. Here, Auvray et al. report Raman scattering evidence of enhanced electronic nematic fluctuations near the endpoint of the pseudogap phase in Bi\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${}_{2}$$\end{document}2Sr\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${}_{2}$$\end{document}2CaCu\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${}_{2}$$\end{document}2O\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${}_{8+\delta }$$\end{document}8+δ.

Dynamic trajectories of volatile and non-volatile specialised metabolites in 'overnight' fragrant flowers of Murraya paniculata

Ephemeral flowers, especially nocturnal ones, usually emit characteristic scent profiles within their post-anthesis lifespans of a few hours. Whether these flowers exhibit temporal variability in the composition and profile of volatile and non-volatile specialised metabolites has received little attention. Flowers of Murraya paniculata bloom in the evenings during the summer and monsoon, and their sweet, intense fragrance enhances the plant's value as an ornamental. We aimed to investigate profiles of both volatile and non-volatile endogenous specialised metabolites (ESM) in nocturnal ephemeral flowers of M. paniculata to examine whether any biochemically diverse groups of ESM follow distinct patterns of accumulation while maintaining synchrony with defensive physiological functions. Targeted ESM contents of M. paniculata flowers were profiled at ten time points at 2-h intervals, starting from late bud stage (afternoon) up to the start of petal senescence (mid-morning). Emitted volatiles were monitored continuously within the whole 20-h period using headspace sampling. The ESM contents were mapped by time point to obtain a highly dynamic and biochemically diverse profile. Relative temporal patterns of ESM accumulation indicated that the active fragrance-emitting period might be divided into 'early bloom', 'mid-bloom' and 'late bloom' phases. Early and late bloom phases were characterised by high free radical generation, with immediate enhancement of antioxidant enzymes and phenolic compounds. The mid-bloom phase was relatively stable and dedicated to maximum fragrance emission, with provision for strong terpenoid-mediated defence against herbivores. The late bloom phase merged into senescence with the start of daylight; however, even the senescent petals continued to emit fragrance to attract diurnal pollinators. Our study suggests that dynamic relations between the different ESM groups regulate the short-term requirements of floral advertisement and phytochemical defence in this ephemeral flower. This study also provided fundamental information on the temporal occurrence of emitted volatiles and internal pools of specialised metabolites in M. paniculata flowers, which could serve as an important model for pollination biology of Rutaceae, which includes many important fruit crops.

Teachers' competence, school policy and social context-HIV prevention needs of primary schools in Kagera, Tanzania

Sub-Saharan Africa carries a high burden of the HIV epidemic, with young adults being particularly affected. Well-designed school-based HIV prevention interventions can contribute to establishing protective behaviour. The aim of this study was to explore the needs of primary school students and teachers in the region of Kagera, Tanzania, regarding an HIV prevention intervention in the primary school setting. The needs assessment was structured according to the PRECEDE component of the PRECEDE-PROCEED model. Qualitative data was collected in six focus group discussions with primary school students and teachers. Key informant interviews with seven experts were conducted. We employed qualitative content analysis to analyse data in MAXQDA. The findings suggest that teachers need to be adequately trained to provide HIV and sex education and to support HIV-positive students. Enabling structural factors, such as an appropriate syllabus, are required. Stigmatization has been reported a major barrier to HIV prevention in schools. Teachers and students identified a more trustful relationship between each other as well as to legal guardians of children as a basis for HIV prevention. These findings will inform the development of a tailored HIV prevention intervention.

Die Anzahl verschlüsselter Diagnosen in einem dokumentationsgerechten Krankenblatt für internistische Patienten

Anfang 1963 wurde in der Medizinischen Universitäts-Klinik Greifswald die Krankenblatt-Dokumentation mit Maschinenlochkarten eingeführt; der dafür entwickelte Krankenblattkopf gestattet die Verschlüsselung von maximal 6 Diagnosen.

Die vorliegende Arbeit ist hauptsächlich statistischen Untersuchungen über die Verteilung der verschlüsselten Diagnosen auf Diagnosengruppen und Altersklassen gewidmet. Sie lassen nach Ansicht der Verfasser den Schluß zu, daß in einem dokumentationsgerechten Krankenblattkopf für internistische Patienten vier Diagnosen-Felder ausreichen.

Abschließend wird kurz das Problem der Krankenblattbearbeitung diskutiert und auf die Bedeutung von Dokumentationsfachkräften hingewiesen.

The ubiquitin ligase Cullin5SOCS2 regulates NDR1/STK38 stability and NF-κB transactivation

SOCS2 is a pleiotropic E3 ligase. Its deficiency is associated with gigantism and organismal lethality upon inflammatory challenge. However, mechanistic understanding of SOCS2 function is dismal due to our unawareness of its protein substrates. We performed a mass spectrometry based proteomic profiling upon SOCS2 depletion and yield quantitative data for ~4200 proteins. Through this screen we identify a novel target of SOCS2, the serine-threonine kinase NDR1. Over-expression of SOCS2 accelerates turnover, while its knockdown stabilizes, endogenous NDR1 protein. SOCS2 interacts with NDR1 and promotes its degradation through K48-linked ubiquitination. Functionally, over-expression of SOCS2 antagonizes NDR1-induced TNFα-stimulated NF-κB activity. Conversely, depletion of NDR1 rescues the effect of SOCS2-deficiency on TNFα-induced NF-κB transactivation. Using a SOCS2^−/− mice model of colitis we show that SOCS2-deficiency is pro-inflammatory and negatively correlates with NDR1 and nuclear p65 levels. Lastly, we provide evidence to suggest that NDR1 acts as an oncogene in prostate cancer. To the best of our knowledge, this is the first report of an identified E3 ligase for NDR1. These results might explain how SOCS2-deficiency leads to hyper-activation of NF-κB and downstream pathological implications and posits that SOCS2 induced degradation of NDR1 may act as a switch in restricting TNFα-NF-κB pathway.

Publisher's Note: Effects of Lifshitz Transitions on Charge Transport in Magnetic Phases of Fe-Based Superconductors [Phys. Rev. Lett. 114, 097003 (2015)]

This corrects the article DOI: 10.1103/PhysRevLett.114.097003.

Charge-induced nematicity in FeSe

The spontaneous appearance of nematicity, a state of matter that breaks rotation but not translation symmetry, is one of the most intriguing properties of the iron-based superconductors (Fe SC), and has relevance for the cuprates as well. Establishing the critical electronic modes behind nematicity remains a challenge, however, because their associated susceptibilities are not easily accessible by conventional probes. Here, using FeSe as a model system, and symmetry-resolved electronic Raman scattering as a probe, we unravel the presence of critical charge nematic fluctuations near the structural/nematic transition temperature, [Formula: see text] 90 K. The diverging behavior of the associated nematic susceptibility foretells the presence of a Pomeranchuk instability of the Fermi surface with d-wave symmetry. The excellent scaling between the observed nematic susceptibility and elastic modulus data demonstrates that the structural distortion is driven by this d-wave Pomeranchuk transition. Our results make a strong case for charge-induced nematicity in FeSe.

Nematic Resonance in the Raman Response of Iron-Based Superconductors

In a fully gapped superconductor the electronic Raman response has a pair-breaking peak at twice the superconducting gap Δ, if the Bogoliubov excitations are uncorrelated. Motivated by the iron based superconductors, we study how this peak is modified if the superconducting phase hosts a nematic-structural quantum critical point. We show that, upon approaching this point by tuning, e.g., doping, the growth of nematic correlations between the quasiparticles transforms the pair-breaking peak into a nematic resonance. The mode energy is below 2Δ, and stays finite at the quantum critical point, where its spectral weight is sharply enhanced. The latter is consistent with recent experiments on electron-doped iron based superconductors and provides direct evidence of nematic correlations in their superconducting phases.

Co-morbidity of Obsessive-compulsive Disorder and Other Anxiety Disorders with Child and Adolescent Mood Disorders

OBJECTIVE

To assess the co-morbidity of obsessive-compulsive disorder (OCD) and other anxiety disorders in child and adolescent mood disorders.

METHODS

A total of 100 patients aged < 18 years with mood disorders according to the DSM-IV-TR were screened for OCD and other anxiety disorders using Schedule for Affective Disorders and Schizophrenia for School-Age Children-Present and Lifetime version.

RESULTS

The prevalence of co-morbid anxiety disorders was 22%; OCD was present in 4%, and subthreshold obsessive-compulsive symptoms were present in 2%. Among others, 8% had panic disorder, 7% had generalised anxiety disorder, 3% had separation anxiety disorder, and 1% had social phobia; multiple anxiety disorders were present in 3% of patients.

CONCLUSION

Co-morbid anxiety disorder was found in one-fifth of children and adolescents with mood disorder.

Collapse of the normal-state pseudogap at a Lifshitz transition in the Bi(2)Sr(2)CaCu(2)O(8+δ) cuprate superconductor

We report a fine tuned doping study of strongly overdoped Bi_{2}Sr_{2}CaCu_{2}O_{8+δ} single crystals using electronic Raman scattering. Combined with theoretical calculations, we show that the doping, at which the normal-state pseudogap closes, coincides with a Lifshitz quantum phase transition where the active holelike Fermi surface becomes electronlike. This conclusion suggests that the microscopic cause of the pseudogap is sensitive to the Fermi surface topology. Furthermore, we find that the superconducting transition temperature is unaffected by this transition, demonstrating that their origins are different on the overdoped side.

Effects of Lifshitz transition on charge transport in magnetic phases of Fe-based superconductors

The unusual temperature dependence of the resistivity and its in-plane anisotropy observed in the Fe-based superconducting materials, particularly Ba(Fe_{1-x}Co_{x})_{2}As_{2}, has been a long-standing puzzle. Here, we consider the effect of impurity scattering on the temperature dependence of the average resistivity within a simple two-band model of a dirty spin density wave metal. The sharp drop in resistivity below the Néel temperature T_{N} in the parent compound can only be understood in terms of a Lifshitz transition following Fermi surface reconstruction upon magnetic ordering. We show that the observed resistivity anisotropy in this phase, arising from nematic defect structures, is affected by the Lifshitz transition as well.

OTUB1 de-ubiquitinating enzyme promotes prostate cancer cell invasion in vitro and tumorigenesis in vivo

Background

Ubiquitination is a highly dynamic and reversible process with a central role in cell homeostasis. Deregulation of several deubiquitinating enzymes has been linked to tumor development but their specific role in prostate cancer progression remains unexplored.

Methods

RNAi screening was used to investigate the role of the ovarian tumor proteases (OTU) family of deubiquitinating enzymes on the proliferation and invasion capacity of prostate cancer cells. RhoA activity was measured in relation with OTUB1 effects on prostate cancer cell invasion. Tumor xenograft mouse model with stable OTUB1 knockdown was used to investigate OTUB1 influence in tumor growth.

Results

Our RNAi screening identified OTUB1 as an important regulator of prostate cancer cell invasion through the modulation of RhoA activation. The effect of OTUB1 on RhoA activation is important for androgen-induced repression of p53 expression in prostate cancer cells. In localized prostate cancer tumors OTUB1 was found overexpressed as compared to normal prostatic epithelial cells. Prostate cancer xenografts expressing reduced levels of OTUB1 exhibit reduced tumor growth and reduced metastatic dissemination in vivo.

Conclusions

OTUB1 mediates prostate cancer cell invasion through RhoA activation and promotes tumorigenesis in vivo. Our results suggest that drugs targeting the catalytic activity of OTUB1 could potentially be used as therapeutics for metastatic prostate cancer.

Electronic supplementary material

The online version of this article (doi:10.1186/s12943-014-0280-2) contains supplementary material, which is available to authorized users.

A CHIPotle in physiology and disease

The carboxy-terminus of Hsc70 interacting protein (CHIP) is known to function as a chaperone associated E3 ligase for several proteins and regulates a variety of physiological processes. Being a connecting link between molecular chaperones and 26S proteasomes, it is widely regarded as the central player in the cellular protein quality control system. Recent analyses have provided new insights on the biochemical and functional dynamics of CHIP. In this review article, we give a comprehensive account of our current knowledge on the biology of CHIP, which apart from shedding light on fundamental biological questions promises to provide a potential target for therapeutic intervention.

Emergent defect states as a source of resistivity anisotropy in the nematic phase of iron pnictides

We consider the role of potential scatterers in the nematic phase of Fe-based superconductors above the transition temperature to the (π, 0) magnetic state but below the orthorhombic structural transition. The anisotropic spin fluctuations in this region can be frozen by disorder, to create elongated magnetic droplets whose anisotropy grows as the magnetic transition is approached. Such states act as strong anisotropic defect potentials that scatter with much higher probability perpendicular to their length than parallel, although the actual crystal symmetry breaking is tiny. We calculate the scattering potentials, relaxation rates, and conductivity in this region and show that such emergent defect states are essential for the transport anisotropy observed in experiments.

Current Understanding on EGFR and Wnt/β-Catenin Signaling in Glioma and Their Possible Crosstalk

Glioblastoma multiformes (GBMs) are extensively heterogeneous at both cellular and molecular levels. Current therapeutic strategies include targeting of key signaling molecules using pharmacological inhibitors in combination with genotoxic agents such as temozolomide. In spite of all efforts, the prognosis of glioma patients remains dismal. Therefore, a proper understanding of individual molecular pathways responsible for the progression of GBM is necessary. The epidermal growth factor receptor (EGFR) pathway is probably the most significant signaling pathway clinically implicated in glioma. Not surprisingly, anti-EGFR therapies mostly prevail for therapeutic purposes. The Wnt/β-catenin pathway is well implicated in multiple tumors; however, its role in glioma has only recently started to emerge. We give a concise account of the current understanding of the role of both these pathways in glioma. Last, taking evidences from a limited literature, we outline a number of points where these pathways intersect each other and put forward the possibility of combinatorially targeting them for treatment of glioma.

Observation of incipient charge nematicity in Ba(Fe(1-x)Co(x))2As2

Using electronic Raman spectroscopy, we report direct measurements of charge nematic fluctuations in the tetragonal phase of strain-free Ba(Fe(1-x)Co(x))2As2 single crystals. The strong enhancement of the Raman response at low temperatures unveils an underlying charge nematic state that extends to superconducting compositions and which has hitherto remained unnoticed. Comparison between the extracted charge nematic susceptibility and the elastic modulus allows us to disentangle the charge contribution to the nematic instability, and to show that charge nematic fluctuations are weakly coupled to the lattice.

Prognostic and therapeutic relevance of FLIP and procaspase-8 overexpression in non-small cell lung cancer

Non-small cell lung carcinoma remains by far the leading cause of cancer-related deaths worldwide. Overexpression of FLIP, which blocks the extrinsic apoptotic pathway by inhibiting caspase-8 activation, has been identified in various cancers. We investigated FLIP and procaspase-8 expression in NSCLC and the effect of HDAC inhibitors on FLIP expression, activation of caspase-8 and drug resistance in NSCLC and normal lung cell line models. Immunohistochemical analysis of cytoplasmic and nuclear FLIP and procaspase-8 protein expression was carried out using a novel digital pathology approach. Both FLIP and procaspase-8 were found to be significantly overexpressed in tumours, and importantly, high cytoplasmic expression of FLIP significantly correlated with shorter overall survival. Treatment with HDAC inhibitors targeting HDAC1-3 downregulated FLIP expression predominantly via post-transcriptional mechanisms, and this resulted in death receptor- and caspase-8-dependent apoptosis in NSCLC cells, but not normal lung cells. In addition, HDAC inhibitors synergized with TRAIL and cisplatin in NSCLC cells in a FLIP- and caspase-8-dependent manner. Thus, FLIP and procaspase-8 are overexpressed in NSCLC, and high cytoplasmic FLIP expression is indicative of poor prognosis. Targeting high FLIP expression using HDAC1–3 selective inhibitors such as entinostat to exploit high procaspase-8 expression in NSCLC has promising therapeutic potential, particularly when used in combination with TRAIL receptor-targeted agents.

Orbital order and Hund's rule frustration in Kondo lattices

We analyze a microscopic origin of the Kondo effect-assisted orbital order in heavy-fermion materials. By studying the periodic two-orbital Anderson model with two local electrons, we show that frustration of Hund's rule coupling due to the Kondo effect leads to an incommensurate spiral orbital and magnetic order, which exists only inside the Kondo screened (heavy-electron) phase. This spiral state can be observed in neutron and resonant x-ray scattering measurements in U- and Pr-based heavy-fermion compounds, and realized in cold atomic gases, e.g., fermionic 173Yb.

Equivalence of single-particle and transport lifetimes from hybridization fluctuations

Single band theories of quantum criticality successfully describe a single-particle lifetime with non-Fermi liquid temperature dependence, but they fail to obtain a charge transport rate with the same dependence unless the interaction is assumed to be momentum independent. Here we demonstrate that a quantum critical material, with a long-range mode that transmutes electrons between light and heavy bands, exhibits a quasilinear temperature dependence for both the single-particle and the charge transport lifetimes, despite the strong momentum dependence of the interaction.

Acquired differential regulation of caspase-8 in cisplatin-resistant non-small-cell lung cancer

Failure to efficiently induce apoptosis contributes to cisplatin resistance in non-small-cell lung cancer (NSCLC). Although BCL-2-associated X protein (BAX) and BCL-2 antagonist killer (BAK) are critical regulators of the mitochondrial apoptosis pathway, their requirement has not been robustly established in relation to cisplatin. Here, we show that cisplatin can efficiently bypass mitochondrial apoptosis block caused by loss of BAX and BAK, via activation of the extrinsic death receptor pathway in some model cell lines. Apoptosis resistance following cisplatin can only be observed when both extrinsic and intrinsic pathways are blocked, consistent with redundancy between mitochondrial and death receptor pathways in cisplatin-induced apoptosis. In H460 NSCLC cells, caspase-8 cleavage was shown to be induced by cisplatin and is dependent on death receptor 4, death receptor 5, Fas-associated protein with death domain, acid sphingomyelinase and ceramide synthesis. In contrast, cisplatin-resistant cells fail to activate caspase-8 via this pathway despite conserving sensitivity to death ligand-driven activation. Accordingly, caspase-8 activation block acquired during cisplatin resistance, can be bypassed by death receptor agonism.

The chaperone-assisted E3 ligase C terminus of Hsc70-interacting protein (CHIP) targets PTEN for proteasomal degradation

The tumor suppressor, PTEN is key to the regulation of diverse cellular processes, making it a prime candidate to be tightly regulated. The PTEN level is controlled in a major way by E3 ligase-mediated degradation through the Ubiquitin-Proteasome System (UPS). Nedd 4-1, XIAP, and WWP2 have been shown to maintain PTEN turnover. Here, we report that CHIP, the chaperone-associated E3 ligase, induces ubiquitination and regulates the proteasomal turnover of PTEN. It was apparent from our findings that PTEN transiently associates with the molecular chaperones and thereby gets diverted to the degradation pathway through its interaction with CHIP. The TPR domain of CHIP and parts of the N-terminal domain of PTEN are required for their interaction. Overexpression of CHIP leads to elevated ubiquitination and a shortened half-life of endogenous PTEN. On the other hand, depletion of endogenous CHIP stabilizes PTEN. CHIP is also shown to regulate PTEN-dependent transcription presumably through its down-regulation. PTEN shared an inverse correlation with CHIP in human prostate cancer patient samples, thereby triggering the prospects of a more complex mode of PTEN regulation in cancer.

Magnetoelastic quantum fluctuations and phase transitions in the iron superconductors

We examine the relevance of magnetoelastic coupling to describe the complex magnetic and structural behavior of the different classes of the iron superconductors. We model the system as a two-dimensional metal whose magnetic excitations interact with the distortions of the underlying square lattice. Going beyond the mean field, we find that quantum fluctuation effects can explain two unusual features of these materials that have attracted considerable attention: first, why iron telluride orders magnetically at a non-nesting wave vector (π/2,π/2) and not at the nesting wave vector (π,0) as in the iron arsenides, even though the nominal band structures of both these systems are similar, and second, why the (π,0) magnetic transition in the iron arsenides is often preceded by an orthorhombic structural transition. These are robust properties of the model, independent of microscopic details, and they emphasize the importance of the magnetoelastic interaction.

Obatoclax induces Atg7-dependent autophagy independent of beclin-1 and BAX/BAK

Direct pharmacological targeting of the anti-apoptotic B-cell lymphoma-2 (BCL-2) family is an attractive therapeutic strategy for treating cancer. Obatoclax is a pan-BCL-2 family inhibitor currently in clinical development. Here we show that, although obatoclax can induce mitochondrial apoptosis dependent on BCL-2 associated x protein/BCL-2 antagonist killer (BAX/BAK) consistent with its on-target pharmacodynamics, simultaneous silencing of both BAX and BAK did not abolish acute toxicity or loss of clonogenicity. This is despite complete inhibition of apoptosis. Obatoclax dramatically reduced viability without inducing loss of plasma membrane integrity. This was associated with rapid processing of light chain-3 (LC3) and reduction of S6 kinase phosphorylation, consistent with autophagy. Dramatic ultrastructural vacuolation, not typical of autophagy, was also induced. Silencing of beclin-1 failed to prevent LC3 processing, whereas knockout of autophagy-related (Atg)7 abolished LC3 processing but failed to prevent obatoclax-induced loss of clonogenicity or ultrastructural changes. siRNA silencing of Atg7 in BAX/BAK knockout mouse embryonic fibroblasts did not prevent obatoclax-induced loss of viability. Cells selected for obatoclax resistance evaded apoptosis independent of changes in BCL-2 family expression and displayed reduced LC3 processing. In summary, obatoclax exhibits BAX- and BAK-dependent and -independent mechanisms of toxicity and activation of autophagy. Mechanisms other than autophagy and apoptosis are blocked in obatoclax resistant cells and contribute significantly to obatoclax's anticancer efficacy.

Prenatal infection decreases calbindin, decreases Purkinje cell volume and density and produces long-term motor deficits in Sprague-Dawley rats

The cerebellum is involved in the control of motor functions with Purkinje cells serving as the only output from the cerebellum. Purkinje cells are important targets for toxic substances and are vulnerable to prenatal insults. Intrauterine infection (IUI) has been shown to selectively target the developing cerebral white matter through lesioning, necrosis and inflammatory cytokine activation. Developmental and cognitive delays have been associated with animal models of IUI. The aim of this study was to determine if IUI leads to damage to Purkinje cells in the developing cerebellum and if any damage is associated with decreases in calbindin and motor behaviors in surviving pups. Pregnant rats were injected with Escherichia coli (1 × 10⁵ colony-forming units) or sterile saline at gestational day 17. Beginning at postnatal day (PND) 2, the pups were subjected to a series of developmental tests to examine developmental milestones. At PND 16, some pups were sacrificed and their brains extracted and processed for histology or protein studies. Hematoxylin and eosin (HE) staining was done to examine the general morphology of the Purkinje cells and to examine Purkinje cell density, area and volume. Calbindin expression was examined in the cerebellum via immunohistochemistry and Western blot techniques. The remaining rat pups were used to examine motor coordination and balance on a rotating rotarod at the prepubertal and adult ages. Prenatal E. coli injection did not significantly change birth weight or delivery time, but did delay surface righting and negative geotaxis in pups. Pups in the E. coli group also had a decrease in the number of Purkinje cells, as well as a decrease in Purkinje cell density and volume. HE staining demonstrated a change in Purkinje cell morphology. Calbindin expression was decreased in rats from the E. coli group as well. Locomotor tests indicated that while there were no significant changes in gross motor activity, motor coordination and balance was impaired in both prepubertal and adult rats from the E. coli group. In this model of IUI, we observed changes in Purkinje cell development which were associated with alterations in cerebellum-dependent motor behaviors. The decreases in calbindin and Purkinje cells were associated with developmental delays. These data further support the importance of IUI in brain development.

Kondo breakdown and hybridization fluctuations in the kondo-heisenberg lattice

We study the deconfined quantum critical point of the Kondo-Heisenberg lattice in three dimensions using a fermionic representation for the localized spins. The mean-field phase diagram exhibits a zero temperature quantum critical point separating a spin liquid phase where the hybridization vanishes and a Kondo phase where it does not. Two solutions can be stabilized in the Kondo phase: namely, a uniform hybridization when the band masses of the conduction electrons and the spinons have the same sign, and a modulated one when they have opposite sign. For the uniform case, we show that above a very small temperature scale, the critical fluctuations associated with the vanishing hybridization have dynamical exponent z=3, giving rise to a resistivity that has a TlogT behavior. We also find that the specific heat coefficient diverges logarithmically in temperature, as observed in a number of heavy fermion metals.

Quantum critical end point for the Kondo volume collapse model

The Kondo volume collapse describes valence transitions in f-electron metals and is characterized by a line of first order transitions in the pressure-temperature phase plane terminated at critical end points. We analyze the quantum critical end point, when the lower end point is tuned to T=0, and determine the specific heat, thermal expansion, and compressibility. We find that the inclusion of quantum critical fluctuations leads to a novel bifurcation of the first order phase line. Finally, we show that critical strain fluctuations can cause both, superconductivity and non-Fermi liquid behavior near the critical point.

Case-control study for risk factors for Q Fever in southwest England and Northern Ireland

Q fever (Coxiella burnetti) is thought to account for 1% (700 cases) of community acquired pneumonia in the United Kingdom each year, and can result in serious complications such as endocarditis. Although outbreaks have frequently been reported worldwide, the causes are often not clearly identified and there have been few studies of risk factors in sporadic cases. We conducted a matched case-control study. Cases of acute Q fever in people aged over 15 years in southwest England and Northern Ireland were identified from January 2002 to December 2004. Controls were matched for age, sex and the general practice at which they were registered. Questionnaires asking about contact with animals, and leisure and work activities, were posted to cases and controls. Questionnaires were completed by 39/50 (78%) of the cases and 90/180 (50%) of the controls. In the single variable analysis, occupational exposure to animals or animal products was the only risk factor associated with cases at the 5% level (P=0.05, odds ratio (OR) 3.4). Long term illness appeared to be significantly protective (P=0.03, OR 0.3). In multivariable analysis the strength of association between occupational exposure and illness remained high (OR 3.6, 95% confidence interval (CI) 0.9 to 14.8) and smoking emerged as a possible risk factor. This is the first case-control study to identify occupational exposure to animals or animal products as the most likely route of infection in sporadic cases as opposed to outbreaks.

Pre-operative plasma erythropoietin concentration and survival following surgery for non-small cell lung cancer

BACKGROUND

Suppression of the effect of the hormone erythropoietin (EPO) on the bone marrow, and an inadequate EPO response to anaemia have been shown to be factors in the genesis of cancer related anaemia. Low haemoglobin (Hb) concentration pre-operatively has been shown to have prognostic significance in patients with surgically resected NSCLC. This study investigates the relationship between pre-operative EPO and survival in patients having surgery for NSCLC.

METHODS

Pre-operative plasma EPO concentration and haemoglobin concentration were analysed in patients undergoing surgery for NSCLC between April 1998 and January 1999. Full follow-up was available for all patients.

RESULTS

Forty two patients were included. Median EPO concentration was 9.4 mIU/ml, range (3.7-56.4) with 17 patients (40.4%) having values above the normal range. Median haemoglobin concentration was 13.3g/dl (range 8.5-16.8) with 15 patients (26%) anaemic pre-operatively. Pathological staging revealed 17 (40.4%) patients with stage I, 6 (14.3%) with stage II, 19 (45.3%) with stage III disease. Ten patients had irresectable disease. There was a significant difference in median EPO but not haemoglobin concentration, between the different pathological stages. Survival was significantly lower in patients with pre-operative EPO >10.5 mIU.

CONCLUSIONS

Raised pre-operative EPO is associated with reduced survival in patients having surgery for NSCLC. Its measurement should be considered in the pre-operative assessment of patients undergoing surgery for NSCLC. Further research is required to further investigate the biological relationship between EPO and NSCLC.