Label-free enrichment of adrenal cortical progenitor cells using inertial microfluidics.

Passive and label-free isolation of viable target cells based on intrinsic biophysical cellular properties would allow for cost savings in applications where molecular biomarkers are known as well as potentially enable the separation of cells with little-to-no known molecular biomarkers. We have demonstrated the purification of adrenal cortical progenitor cells from digestions of murine adrenal glands utilizing hydrodynamic inertial lift forces that single cells and multicellular clusters differentially experience as they flow through a microchannel. Fluorescence staining, along with gene expression measurements, confirmed that populations of cells collected in different outlets were distinct from one another. Furthermore, primary murine cells processed through the device remained highly viable and could be cultured for 10 days in vitro. The proposed target cell isolation technique can provide a practical means to collect significant quantities of viable intact cells required to translate stem cell biology to regenerative medicine in a simple label-free manner

Mechanical Resonances of Mobile Impurities in a One-Dimensional Quantum Fluid

We study a one-dimensional interacting quantum liquid hosting a pair of mobile impurities causing backscattering. We determine the effective retarded interaction between the two impurities mediated by the liquid. We show that for strong backscattering this interaction gives rise to resonances and antiresonances in the finite-frequency mobility of the impurity pair. At the antiresonances, the two impurities remain at rest even when driven by a (small) external force. At the resonances, their synchronous motion follows the external drive in phase and reaches maximum amplitude. Using a perturbative renormalization group analysis in quantum tunneling across the impurities, we study the range of validity of our model. We predict that these mechanical antiresonances are observable in experiments on ultracold atom gases confined to one dimension

Initial development and biomass allocation in seedlings of Brosimum rubescens Taub. (Moraceae) at different shading levels

Florestas monodominantes de Brosimum rubescens Taub. (Moraceae) ocorrem na zona de transição Cerrado/Amazônia e encontram-se ameaçadas pela extração da madeira. Dentre as possíveis causas de monodominância destaca-se a disponibilidade de luz, de modo que o objetivo deste trabalho foi testar os efeitos no crescimento e na assimilação de CO2 de diferentes níveis de sombreamento em condições naturais e em viveiro. Em viveiro, os tratamentos foram 0, 30, 50, 70 e 90% de sombreamento e na floresta foram avaliadas plantas jovens crescendo sob o dossel e em clareira. A taxa de assimilação de CO2 em resposta a variações na intensidade luminosa foi medida em plantas jovens sob três condições de sombreamento. As plantas que cresceram sob o dossel fechado apresentaram taxas de crescimento relativo menores do que aquelas que cresceram na clareira. Aos 21 meses, o maior valor de massa seca total (9,46 g) foi encontrado sob 50% de sombreamento, representando um acúmulo de biomassa 144% superior ao tratamento sob 90%. Em todos os tratamentos e amostragens, a partição foi massa seca da raiz > folhas > caule. A menor taxa fotossintética máxima (Amáx= 3,46 µmol m-2 s1) foi observada para 90% de sombreamento e a maior (Amáx= 7,89 µmol m-2 s-1) foi registrada sob 30% de sombreamento. Clareiras provavelmente desempenham um papel importante na manutenção da monodominância, uma vez que B. rubescens apresentou plasticidade para diferentes condições de luminosidade e maior crescimento nos níveis intermediários de sombreamento.Monodominant forests of Brosimum rubescens Taub. (Moraceae) occur at the Cerrado/Amazonia boundary and are threatened by logging. Light is considered an important determinant for monodominance in forests, so the aim of this study was to analyze initial growth at shading levels of 0, 30, 50, 70 and 90% in the nursery, in a forest gap, and also at a closed canopy site. Photosynthesis was measured in seedlings at three shading levels. Seedlings under a closed canopy showed lower relative growth rates in comparison to seedlings growing in a nearby gap. At 21 months of age, the highest total dry mass of 9.46 g was measured at 50% shading. This represents a biomass accumulation of 144% over that found at 90% shading. For all treatments in every assessment the partitioning was dry matter of roots > leaves > stems. The lowest maximum photosynthesis rate (Amax= 3.46 µmol m-2 s-1) was recorded at 90% shading and the highest (Amax= 7.89 µmol m-2 s-1) was recorded at 30% shading. Gaps seem to play an important role in maintaining monodominance since B. rubescens showed some plasticity regarding light conditions and grew better at intermediate shading levels

Non-invasive intradialytic percutaneous perfusion monitoring: a view to the heart through the skin

IntroductionThe life-sustaining treatment of hemodialysis (HD) induces recurrent and cumulative systemic circulatory stress resulting in cardiovascular injury. These recurrent insults compound preexisting cardiovascular sequalae leading to the development of myocardial injury and resulting in extremely high morbidity/mortality. This is largely a consequence of challenged microcirculatory flow within the myocardium (evidenced by detailed imaging-based studies). Currently, monitoring during HD is performed at the macrovascular level. Non-invasive monitoring of organ perfusion would allow the detection and therapeutic amelioration of this pathophysiological response to HD. Non-invasive percutaneous perfusion monitoring of the skin (using photoplethysmography—PPG) has been shown to be predictive of HD-induced myocardial stunning (a consequence of segmental ischemia). In this study, we extended these observations to include a dynamic assessment of skin perfusion during HD compared with directly measured myocardial perfusion during dialysis and cardiac contractile function.MethodsWe evaluated the intradialytic microcirculatory response in 12 patients receiving conventional HD treatments using continuous percutaneous perfusion monitoring throughout HD. Cardiac echocardiography was performed prior to the initiation of HD, and again at peak-HD stress, to assess the development of regional wall motion abnormalities (RWMAs). Myocardial perfusion imaging was obtained at the same timepoints (pre-HD and peak-HD stress), utilizing intravenous administered contrast and a computerized tomography (CT)-based method. Intradialytic changes in pulse strength (derived from PPG) were compared with the development of HD-induced RWMAs (indicative of myocardial stunning) and changes in myocardial perfusion.ResultsWe found an association between the lowest pulse strength reduction (PPG) and the development of RWMAs (p = 0.03) and also with changes in global myocardial perfusion (CT) (p = 0.05). Ultrafiltration rate (mL/kg/hour) was a significant driver of HD-induced circulatory stress [(associated with the greatest pulse strength reduction (p = 0.01), a reduction in global myocardial perfusion (p = 0.001), and the development of RWMAs (p = 0.03)].DiscussionPercutaneous perfusion monitoring using PPG is a useful method of assessing intradialytic hemodynamic stability and HD-induced circulatory stress. The information generated at the microcirculatory level of the skin is reflective of direct measures of myocardial perfusion and the development of HD-induced myocardial stunning. This approach for the detection and management of HD-induced cardiac injury warrants additional evaluation

Pink1 and Parkin regulate Drosophila intestinal stem cell proliferation during stress and aging.

Intestinal stem cells (ISCs) maintain the midgut epithelium in Drosophila melanogaster Proper cellular turnover and tissue function rely on tightly regulated rates of ISC division and appropriate differentiation of daughter cells. However, aging and epithelial injury cause elevated ISC proliferation and decreased capacity for terminal differentiation of daughter enteroblasts (EBs). The mechanisms causing functional decline of stem cells with age remain elusive; however, recent findings suggest that stem cell metabolism plays an important role in the regulation of stem cell activity. Here, we investigate how alterations in mitochondrial homeostasis modulate stem cell behavior in vivo via RNA interference-mediated knockdown of factors involved in mitochondrial dynamics. ISC/EB-specific knockdown of the mitophagy-related genes Pink1 or Parkin suppresses the age-related loss of tissue homeostasis, despite dramatic changes in mitochondrial ultrastructure and mitochondrial damage in ISCs/EBs. Maintenance of tissue homeostasis upon reduction of Pink1 or Parkin appears to result from reduction of age- and stress-induced ISC proliferation, in part, through induction of ISC senescence. Our results indicate an uncoupling of cellular, tissue, and organismal aging through inhibition of ISC proliferation and provide insight into strategies used by stem cells to maintain tissue homeostasis despite severe damage to organelles

Probabilistic Programming with Densities in SlicStan: Efficient, Flexible, and Deterministic

Stan is a probabilistic programming language that has been increasingly used for real-world scalable projects. However, to make practical inference possible, the language sacrifices some of its usability by adopting a block syntax, which lacks compositionality and flexible user-defined functions. Moreover, the semantics of the language has been mainly given in terms of intuition about implementation, and has not been formalised. This paper provides a formal treatment of the Stan language, and introduces the probabilistic programming language SlicStan --- a compositional, self-optimising version of Stan. Our main contributions are: (1) the formalisation of a core subset of Stan through an operational density-based semantics; (2) the design and semantics of the Stan-like language SlicStan, which facilities better code reuse and abstraction through its compositional syntax, more flexible functions, and information-flow type system; and (3) a formal, semantic-preserving procedure for translating SlicStan to Stan

Modeling precision treatment of breast cancer

Background: First-generation molecular profiles for human breast cancers have enabled the identification of features that can predict therapeutic response; however, little is known about how the various data types can best be combined to yield optimal predictors. Collections of breast cancer cell lines mirror many aspects of breast cancer molecular pathobiology, and measurements of their omic and biological therapeutic responses are well-suited for development of strategies to identify the most predictive molecular feature sets. Results: We used least squares-support vector machines and random forest algorithms to identify molecular features associated with responses of a collection of 70 breast cancer cell lines to 90 experimental or approved therapeutic agents. The datasets analyzed included measurements of copy number aberrations, mutations, gene and isoform expression, promoter methylation and protein expression. Transcriptional subtype contributed strongly to response predictors for 25% of compounds, and adding other molecular data types improved prediction for 65%. No single molecular dataset consistently out-performed the others, suggesting that therapeutic response is mediated at multiple levels in the genome. Response predictors were developed and applied to TCGA data, and were found to be present in subsets of those patient samples. Conclusions: These results suggest that matching patients to treatments based on transcriptional subtype will improve response rates, and inclusion of additional features from other profiling data types may provide additional benefit. Further, we suggest a systems biology strategy for guiding clinical trials so that patient cohorts most likely to respond to new therapies may be more efficiently identified

Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis

Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen–Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase

Physicochemical property distributions for accurate and rapid pairwise protein homology detection

<p>Abstract</p> <p>Background</p> <p>The challenge of remote homology detection is that many evolutionarily related sequences have very little similarity at the amino acid level. Kernel-based discriminative methods, such as support vector machines (SVMs), that use vector representations of sequences derived from sequence properties have been shown to have superior accuracy when compared to traditional approaches for the task of remote homology detection.</p> <p>Results</p> <p>We introduce a new method for feature vector representation based on the physicochemical properties of the primary protein sequence. A distribution of physicochemical property scores are assembled from 4-mers of the sequence and normalized based on the null distribution of the property over all possible 4-mers. With this approach there is little computational cost associated with the transformation of the protein into feature space, and overall performance in terms of remote homology detection is comparable with current state-of-the-art methods. We demonstrate that the features can be used for the task of pairwise remote homology detection with improved accuracy versus sequence-based methods such as BLAST and other feature-based methods of similar computational cost.</p> <p>Conclusions</p> <p>A protein feature method based on physicochemical properties is a viable approach for extracting features in a computationally inexpensive manner while retaining the sensitivity of SVM protein homology detection. Furthermore, identifying features that can be used for generic pairwise homology detection in lieu of family-based homology detection is important for applications such as large database searches and comparative genomics.</p