# Quantitative Biology

## New submissions

[ total of 18 entries: 1-18 ]
[ showing up to 2000 entries per page: fewer | more ]

### New submissions for Tue, 20 Mar 18

[1]
Title: Accurate evaluation of size and refractive index for spherical objects in quantitative phase imaging
Comments: 14 pages, 10 figures, 1 table
Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

Measuring the average refractive index (RI) of spherical objects, such as suspended cells, in quantitative phase imaging (QPI) requires a decoupling of RI and size from the QPI data. This has been commonly achieved by determining the object's radius with geometrical approaches, neglecting light-scattering. Here, we present a novel QPI fitting algorithm that reliably uncouples the RI using Mie theory and a semi-analytical, corrected Rytov approach. We assess the range of validity of this algorithm in silico and experimentally investigate various objects (oil and protein droplets, microgel beads, cells) and noise conditions. In addition, we provide important practical cues for future studies in cell biology.

[2]
Title: Analysis of Triplet Motifs in Biological Signed Oriented Graphs Suggests a Relationship Between Fine Topology and Function
Subjects: Molecular Networks (q-bio.MN)

Background: Networks in different domains are characterized by similar global characteristics while differing in local structures. To further extend this concept, we investigated network regularities on a fine scale in order to examine the functional impact of recurring motifs in signed oriented biological networks. In this work we generalize to signaling net works some considerations made on feedback and feed forward loops and extend them by adding a close scrutiny of Linear Triplets, which have not yet been investigate in detail. Results: We studied the role of triplets, either open or closed (Loops or linear events) by enumerating them in different biological signaling networks and by comparing their significance profiles. We compared different data sources and investigated the fine topology of protein networks representing causal relationships based on transcriptional control, phosphorylation, ubiquitination and binding. Not only were we able to generalize findings that have already been reported but we also highlighted a connection between relative motif abundance and node function. Furthermore, by analyzing for the first time Linear Triplets, we highlighted the relative importance of nodes sitting in specific positions in closed signaling triplets. Finally, we tried to apply machine learning to show that a combination of motifs features can be used to derive node function. Availability: The triplets counter used for this work is available as a Cytoscape App and as a standalone command line Java application. this http URL

[3]
Title: Learning recurrent dynamics in spiking networks
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Learning (cs.LG); Neural and Evolutionary Computing (cs.NE)

Spiking activity of neurons engaged in learning and performing a task show complex spatiotemporal dynamics. While the output of recurrent network models can learn to perform various tasks, the possible range of recurrent dynamics that emerge after learning remains unknown. Here we show that modifying the recurrent connectivity with a recursive least squares algorithm provides sufficient flexibility for synaptic and spiking rate dynamics of spiking networks to produce a wide range of spatiotemporal activity. We apply the training method to learn arbitrary firing patterns, stabilize irregular spiking activity of a balanced network, and reproduce the heterogeneous spiking rate patterns of cortical neurons engaged in motor planning and movement. We identify sufficient conditions for successful learning, characterize two types of learning errors, and assess the network capacity. Our findings show that synaptically-coupled recurrent spiking networks possess a vast computational capability that can support the diverse activity patterns in the brain.

[4]
Title: Eshel Ben-Jacob: A unique individual in the science of collective phenomena
Authors: Herbert Levine
Comments: based on a meeting talk in June 2015; published in Landscapes of Collectivity, MIT Press this https URL
Subjects: Other Quantitative Biology (q-bio.OT); Cell Behavior (q-bio.CB)

Eshel Ben-Jacob, one of the co-organizers of this meeting on collective behavior and one of the pioneers in the field of collective behavior in biology, passed away suddenly just before we convened. This article presents a brief glimpse of Eshel's life-long path through science, seen from the perspective of a decades long collaboration on many disparate yet ultimately connected topics. The article attempts to convey how the concept of self-organization of complex interacting objects into higher order functional units, as evidenced so wonderfully by Eshel's experiments on bacterial colony formation, provides a unifying theme for the study of collective behavior. Our entire field will miss his unique ability to "let the complex become simple".

[5]
Title: Metabolomic signature of type 1 diabetes-induced sensory loss and nerve damage in diabetic neuropathy
Subjects: Cell Behavior (q-bio.CB); Tissues and Organs (q-bio.TO)

Diabetic-induced peripheral neuropathy (DPN) is a diabetic late complication. The molecular mechanisms underlying the pathophysiology of nerve damage & sensory loss remain largely unclear. Recently, alterations in metabolic flux have gained attention a basis for organ damage in diabetes; however, peripheral sensory neurons have not been adequately analyzed. In the present study, we attempted to delineate the role of alteration of metabolic pathways in relation to nerve damage & sensory loss. We employed STZ-injected mouse model of type1 diabetes. To investigate the progression of DPN by behavioral measurements of sensitivity to thermal & mechanical stimuli and quantitative assessment of intraepidermal nerve fiber density. We employed a MS-based screen to address alterations in levels of metabolites in peripheral sciatic nerve (SN) & amino acids (AA) in serum over several months post-STZ administration. Although hyperglycemia & body weight changes occurred early, sensory loss & reduced intraepithelial branching of nociceptive nerves was only evident at 22 wks post-STZ. The longitudinal metabolites screen in SN demonstrated that mice at 12 and 22 wks post-STZ showed an early impairment the tricarboxylic acid. We found that levels of citric acid, ketoglutaric acid, succinic acid, fumaric acid & malic acid were observed to be significantly reduced in SN at 22 wks post-STZ. In addition, we also found the increase in levels of sorbitol & L-Lactate in SN from 12 wks post-STZ injection. AA screen in serum showed that the amino acids Val, Ile and Leu, increased more than 2-fold from 12 wks post-STZ. Similarly, the levels of Tyr, Asn, Ser, His, Ala, & Pro showed progressive increase. Our results indicate that the impaired TCA cycle metabolites in peripheral nerve is the primary cause of shunting metabolic substrate to compensatory pathways which leads to mitochondrial dysfunction & nerve damage.

[6]
Title: The eBDIMS path-sampling server: generation, classification and interactive visualization of protein ensembles and transition pathways in 2D-motion space
Subjects: Biomolecules (q-bio.BM)

The recent rise of cryo-EM and X-ray high-throughput techniques is providing a wealth of new structures trapped in different conformations. Understanding how proteins transition between different conformers, and how they relate to each other in terms of function is not straightforward, and highly depends on the choice of the right set of degrees of freedom. Here we present eBDIMS server, an online tool and software for automatic classification of structural ensembles and reconstruction of transition pathways using coarse-grained (CG) simulations. The server generates CG-pathways between two protein conformations along with a representation in a simplified 2D-motion landscape based on the Principal Components (PCs) from experimental structures. For a conformationally rich ensemble, the PCs provide powerful reaction coordinates for automatic structure classification, detection of on-pathway intermediates and validation of in silico pathways. When the number of available structures is low or sampling is limited, Normal Modes (NMs) provide alternative motion axes for trajectory analysis. The path-generation eBDIMS method is available at a user-friendly website: https://login.biophysics.kth.se/eBDIMS/ or as standalone software. The server incorporates a powerful interactive graphical interface for simultaneous visualization of transition pathways in 2D-motion space and 3D-molecular graphics, which greatly facilitates the exploration of the relationships between different conformations.

### Cross-lists for Tue, 20 Mar 18

[7]  arXiv:1803.06393 (cross-list from stat.AP) [pdf, other]
Title: Phylogeny-based tumor subclone identification using a Bayesian feature allocation model
Subjects: Applications (stat.AP); Tissues and Organs (q-bio.TO)

Tumor cells acquire different genetic alterations during the course of evolution in cancer patients. As a result of competition and selection, only a few subgroups of cells with distinct genotypes survive. These subgroups of cells are often referred to as subclones. In recent years, many statistical and computational methods have been developed to identify tumor subclones, leading to biologically significant discoveries and shedding light on tumor progression, metastasis, drug resistance and other processes. However, most existing methods are either not able to infer the phylogenetic structure among subclones, or not able to incorporate copy number variations (CNV). In this article, we propose SIFA (tumor Subclone Identification by Feature Allocation), a Bayesian model which takes into account both CNV and tumor phylogeny structure to infer tumor subclones. We compare the performance of SIFA with two other commonly used methods using simulation studies with varying sequencing depth, evolutionary tree size, and tree complexity. SIFA consistently yields better results in terms of Rand Index and cellularity estimation accuracy. The usefulness of SIFA is also demonstrated through its application to whole genome sequencing (WGS) samples from four patients in a breast cancer study.

[8]  arXiv:1803.06544 (cross-list from cond-mat.soft) [pdf, ps, other]
Title: Long ligands reinforce biological adhesion under shear flow
Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

In the present work the computer modelling was used to show that longer ligands allow biological cells (e.g. blood platelets) to withstand stronger flows after their adhesion to solid walls. Mechanistic model of polymer-mediated ligand-receptor adhesion between a microparticle (cell) and a flat wall was developed. Theoretical threshold between adherent and non-adherent regimes was derived analytically and approved by the simulations. These results lead to deeper understanding of numerous biophysical processes, e.g. arterial thrombosis, and to the design of new biomimetic colloid-polymer systems.

[9]  arXiv:1803.06935 (cross-list from physics.soc-ph) [pdf]
Title: Mathematical Analysis of Anthropogenic Signatures: The Great Deceleration
Authors: Ron W. Nielsen
Comments: 30 pages, 31 figures, 2 tables, 8991 words
Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)

Distributions of anthropogenic signatures (impacts and activities) are mathematically analysed. The aim is to understand the Anthropocene and to see whether anthropogenic signatures could be used to determine its beginning. A total of 23 signatures were analysed and results are presented in 31 diagrams. Some of these signatures contain undistinguishable natural component but most of them are of purely anthropogenic origin. Great care was taken to identify abrupt accelerations, which could be used to determine the beginning of the Anthropocene. Results of the analysis can be summarised in three conclusions. 1. Anthropogenic signatures cannot be used to determine the beginning of the Anthropocene. 2. There was no abrupt Great Acceleration around 1950 or around any other time. 3. Anthropogenic signatures are characterised by the Great Deceleration in the second half of the 20th century. The Great Deceleration indicates a gradual progress towards a sustainable future.

[10]  arXiv:1803.07063 (cross-list from physics.bio-ph) [pdf, other]
Title: Quantized Dehydration and the Determinants of Selectivity in the NaChBac Bacterial Sodium Channel
Comments: 13 pages 7 figure + Supplemental Information
Subjects: Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)

A discrete electrostatic/diffusion model has been developed to describe the selective permeation of ion channels, based on ionic Coulomb blockade (ICB) and quantised dehydration (QD). It has been applied to describe selectivity phenomena measured in the bacterial NaChBac sodium channel and some of its mutants. Site-directed mutagenesis and the whole-cell patch-clamp technique were used to investigate how the value $Q_f$ of the fixed charge at the selectivity filter (SF) affected both valence and alike-charge selectivity. The new ICB/QD model predicts that increasing ${Q_f}$ should lead to a shift of selectivity sequences towards larger ion sizes and charges, a result that agrees with the present experiments and with earlier work. Comparison of the model with experimental data provides evidence for an {\it effective charge} $Q_f^*$ at the SF that is smaller in magnitude than the nominal $Q_f$ corresponding to the charge on the isolated protein residues. Furthermore, $Q_f^*$ was different for aspartate and glutamate charged rings and also depended on their position within the SF. It is suggested that protonation of the residues within the restricted space is an important factor in significantly reducing the effective charge of the EEEE ring. Values of $Q_f^*$ derived from experiments on the anomalous mole fraction effect (AMFE) agree well with expectations based on the ICB/QD model and have led to the first clear demonstration of the expected ICB oscillations in Ca$^{2+}$ conduction as a function of the fixed charge. Pilot studies of the dependence of Ca$^{2+}$ conduction on pH are consistent with the predictions of the model.

### Replacements for Tue, 20 Mar 18

[11]  arXiv:1706.01015 (replaced) [pdf, other]
Title: The split-and-drift random graph, a null model for speciation
Comments: added Proposition 2.4 and formal proofs of Proposition 2.3 and 2.6
Subjects: Probability (math.PR); Combinatorics (math.CO); Populations and Evolution (q-bio.PE)
[12]  arXiv:1708.08568 (replaced) [pdf, other]
Title: How directional mobility affects biodiversity in rock-paper-scissors models
Subjects: Populations and Evolution (q-bio.PE); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph)
[13]  arXiv:1710.05783 (replaced) [pdf, other]
Title: Molecular dynamics study of T=3 capsid assembly
Authors: D.C. Rapaport
Comments: 18 pages, 10 figures (minor changes)
Subjects: Biomolecules (q-bio.BM)
[14]  arXiv:1710.09793 (replaced) [pdf, other]
Title: Statistical Inference on Tree Swallow Migrations with Random Forests
Comments: 32 pages, 9 figures. Work between Cornell Lab of Ornithology and University of Pittsburgh Department of Statistics. Substantially overhauled all sections for submission to JASA A&CS
Subjects: Populations and Evolution (q-bio.PE); Applications (stat.AP)
[15]  arXiv:1711.10930 (replaced) [pdf, ps, other]
Title: Two types of criticality in the brain
Subjects: Disordered Systems and Neural Networks (cond-mat.dis-nn); Neurons and Cognition (q-bio.NC)
[16]  arXiv:1802.05856 (replaced) [pdf, other]
Title: Algorithmic Complexity and Reprogrammability of Chemical Structure Networks
Subjects: Molecular Networks (q-bio.MN); Computational Engineering, Finance, and Science (cs.CE); Information Theory (cs.IT)
[17]  arXiv:1803.01639 (replaced) [pdf, ps, other]
Title: When do we have the power to detect biological interactions in spatial point patterns?
Comments: Main text 18 pages on 12pt font, 4 figures. Appendix 7 pages
Subjects: Populations and Evolution (q-bio.PE); Methodology (stat.ME)
[18]  arXiv:1803.02626 (replaced) [pdf, other]
Title: Inferring health conditions from fMRI-graph data
Comments: V1: 35 pages, 5 figures, 2 tables. V2: 36 pages, 5 figures, 2 tables; partially rewritten all sections and added references
Subjects: Quantitative Methods (q-bio.QM); Neurons and Cognition (q-bio.NC); Applications (stat.AP)
[ total of 18 entries: 1-18 ]
[ showing up to 2000 entries per page: fewer | more ]

Disable MathJax (What is MathJax?)