Small Compartments Research Articles

The bioavailability of soybean polysaccharides and their metabolites on gut microbiota in the simulator of the human intestinal microbial ecosystem (SHIME)

The present study aimed to investigate the bioavailability of soybean polysaccharides and their metabolites on gut microbiota in the simulator of the human intestinal microbial ecosystem (SHIME). The effects of soybean polysaccharides on probiotics and pathogenic bacteria were investigated in vitro. Our results showed that soybean polysaccharides were only partially degraded in the oral, gastric, and small intestinal compartments of the SHIME. Moreover, the polysaccharides could be mainly broken down and utilized by the gut microbiota in the colon of the SHIME. Soybean polysaccharides could significantly reduce the ratio of Firmicutes to Bacteroidetes at the phylum level. Therefore, the number of beneficial bacteria were noticeably enhanced, and the pathogenic bacteria were inhibited. Furthermore, soybean polysaccharides promoted the growth of probiotics and improved the ability of these probiotics to inhibit pathogenic bacteria. Therefore, soybean polysaccharides could potentially be functional food to prevent disease by promoting gut health.

The bundle sheath of rice is conditioned to play an active role in water transport as well as sulfur assimilation and jasmonic acid synthesis.

Leaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake the rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C3 plants, which represents a key target associated with engineering traits such as C4 photosynthesis into Oryza sativa (rice). To better understand the veins, bundle sheath and mesophyll cells of rice, we used laser capture microdissection followed by deep sequencing. Gene expression of the mesophyll is conditioned to allow coenzyme metabolism and redox homeostasis, as well as photosynthesis. In contrast, the bundle sheath is specialized in water transport, sulphur assimilation and jasmonic acid biosynthesis. Despite the small chloroplast compartment of bundle sheath cells, substantial photosynthesis gene expression was detected. These patterns of gene expression were not associated with the presence or absence of specific transcription factors in each cell type, but were instead associated with gradients in expression across the leaf. Comparative analysis with C3 Arabidopsis identified a small gene set preferentially expressed in the bundle sheath cells of both species. This gene set included genes encoding transcription factors from 14 orthogroups and proteins allowing water transport, sulphate assimilation and jasmonic acid synthesis. The most parsimonious explanation for our findings is that bundle sheath cells from the last common ancestor of rice and Arabidopsis were specialized in this manner, and as the species diverged these patterns of gene expression have been maintained.

Zooplankton mortality effects on the plankton community of the northern Humboldt Current System: sensitivity of a regional biogeochemical model

Abstract. Small pelagic fish off the coast of Peru in the eastern tropical South Pacific (ETSP) support around 10 % of global fish catches. Their stocks fluctuate interannually due to environmental variability which can be exacerbated by fishing pressure. Because these fish are planktivorous, any change in fish abundance may directly affect the plankton and the biogeochemical system. To investigate the potential effects of variability in small pelagic fish populations on lower trophic levels, we used a coupled physical–biogeochemical model to build scenarios for the ETSP and compare these against an already-published reference simulation. The scenarios mimic changes in fish predation by either increasing or decreasing mortality of the model's large and small zooplankton compartments. The results revealed that large zooplankton was the main driver of the response of the community. Its concentration increased under low mortality conditions, and its prey, small zooplankton and large phytoplankton, decreased. The response was opposite, but weaker, in the high mortality scenarios. This asymmetric behaviour can be explained by the different ecological roles of large, omnivorous zooplankton and small zooplankton, which in the model is strictly herbivorous. The response of small zooplankton depended on the antagonistic effects of mortality changes as well as on the grazing pressure by large zooplankton. The results of this study provide a first insight into how the plankton ecosystem might respond if variations in fish populations were modelled explicitly.

BiFC Method Based on Intraorganellar Protein Crowding Detects Oleate-Dependent Peroxisomal Targeting of Pichia pastoris Malate Dehydrogenase.

The maintenance of intracellular NAD+/NADH homeostasis across multiple, subcellular compartments requires the presence of NADH-shuttling proteins, which circumvent the lack of permeability of organelle membranes to these cofactors. Very little is known regarding these proteins in the methylotrophic yeast, Pichia pastoris. During the study of the subcellular locations of these shuttling proteins, which often have dual subcellular locations, it became necessary to develop new ways to detect the weak peroxisomal locations of some of these proteins. We have developed a novel variation of the traditional Bimolecular Fluorescence Complementation (BiFC), called divergent BiFC, to detect intraorganellar colocalization of two noninteracting proteins based on their proximity-based protein crowding within a small subcellular compartment, rather than on the traditional protein–protein interactions expected for BiFC. This method is used to demonstrate the partially peroxisomal location of one such P. pastoris NADH-shuttling protein, malate dehydrogenase B, only when cells are grown in oleate, but not when grown in methanol or glucose. We discuss the mode of NADH shuttling in P. pastoris and the physiological basis of the medium-dependent compartmentalization of PpMdhB.

English

BACKGROUND Intrathoracic mass is a problem faced by the clinicians worldwide which is difficult to diagnose correctly. The mediastinum although a small anatomic compartment, the pathologic processes found in it are diverse. Imaging techniques are very helpful for detection and diagnosing these lesions. The current study was conducted for assessing the diagnostic accuracy and efficacy of computed tomography (CT) guided fine-needle aspiration cytology (FNAC) in the evaluation of various thoracic mass lesions and also to compare the histopathological findings of CT guided FNAC for evaluation of the type of thoracic lesions & its prognosis. METHODS Data for the study was collected from 50 patients referred to the Department of Pathology, in a tertiary care hospital for 16 months from December 2015 to March 2017. RESULTS Among 50 patients with intrathoracic mass, there were 37 men (74 %) and 13 women (26 %). The age of patients with intrathoracic masses in this study varied from 31 to 80 years. The mean age was 55 years. Thirty-two patients were found to have malignant tumours and 18 cases were of benign aetiology. The highest frequency of cases in this study were of adenocarcinoma followed by squamous cell carcinoma. CONCLUSIONS Computed tomography (CT) guided fine-needle aspiration cytology (FNAC) is a cost effective, simple, safe, highly sensitive & specific procedure with high diagnostic accuracy in the diagnosis of intrathoracic mass lesions. It has few complications, rarely requiring active management. KEY WORDS Intrathoracic Mass, Fine-Needle Aspiration Cytology, Pneumothorax, Pneumonectomy, Thoracic Mass Lesions

Macroscopic anatomy, radiography and computed tomography of normal paranasal sinuses of the adult one-humped dromedary (Camelus dromedarius).

In order to improve the current knowledge of the topography and the anatomy of the paranasal sinuses of the one‐humped dromedary (Camelus dromedarius), we applied both conventional and advanced imaging techniques, namely, radiography and computed tomography (CT). Twelve heads of healthy dromedaries were used; eight heads were dissected to obtain skulls for the fenestration of the sinuses, two heads underwent anatomical sections, and two heads were imaged respectively by radiography and CT. Sinus fenestration allowed observation of sinuses and their communications. In each dissected dromedary's head, the frontal sinus is a large compartment delimited by thick partitions. The sphenoid sinus is divided into small compartments by bony plates. The lacrimal sinus occupies a small cavity in the rostro‐medial lacrimal bone of the orbit. In all dissected heads, there was neither palatal sinus nor ventral conchal sinus. Five images obtained by CT were selected with an excellent correspondence with the anatomical sections. These images allowed a good differentiation between bones and sinus cavities. The visualisation of the sinus cavities and their anatomical limits has better quality using the CT compared to the radiography. Radiographic and CT images are therefore very useful for the interpretation of clinical imaging studies of the dromedary's paranasal sinuses.

Quasi-robust control of biochemical reaction networks via stochastic morphing.

One of the main objectives of synthetic biology is the development of molecular controllers that can manipulate the dynamics of a given biochemical network that is at most partially known. When integrated into smaller compartments, such as living or synthetic cells, controllers have to be calibrated to factor in the intrinsic noise. In this context, biochemical controllers put forward in the literature have focused on manipulating the mean (first moment) and reducing the variance (second moment) of the target molecular species. However, many critical biochemical processes are realized via higher-order moments, particularly the number and configuration of the probability distribution modes (maxima). To bridge the gap, we put forward the stochastic morpher controller that can, under suitable timescale separations, morph the probability distribution of the target molecular species into a predefined form. The morphing can be performed at a lower-resolution, allowing one to achieve desired multi-modality/multi-stability, and at a higher-resolution, allowing one to achieve arbitrary probability distributions. Properties of the controller, such as robustness and convergence, are rigorously established, and demonstrated on various examples. Also proposed is a blueprint for an experimental implementation of stochastic morpher.

Compartment Syndrome: an Acute Femoral Stress Fracture in a Young Male Athlete

The incidence of an acute compartment syndrome (ACS) of the thigh is less than 1%. It is most common in the setting of muscle overuse or muscle injury, as well as secondary to trauma, such as a femoral fracture. We present a case of an ACS in a young, healthy, and semiprofessional athlete with normal coagulation who sustained an acute stress fracture of the distal femur. After the initial fracture osteosynthesis, the patient suffered from a compartment syndrome in the right anterior aspect of the distal thigh. Following rapid surgical fasciotomy, the case was uneventful, and he returned to his preinjury sport level without any neurological consequences. This case confirms that ACS in the thigh is rare, but mainly occurs in young males with a large muscle mass due to participation in various athletic programs. We hypothesize that constant muscle over-usage primes for a larger amount of contused and protruding muscle mass in the small femoral compartment. Hence, the fatigued muscle subjects the bone to an increased mechanical force resulting in an overloading process. This ensues the accumulation of femoral microfractures and primes for the occurrence of an increased rate of stress fractures and an ACS in the thigh.

The role of molecular diffusion within dendritic spines in synaptic function.

Spines are tiny nanoscale protrusions from dendrites of neurons. In the cortex and hippocampus, most of the excitatory postsynaptic sites reside in spines. The bulbous spine head is connected to the dendritic shaft by a thin membranous neck. Because the neck is narrow, spine heads are thought to function as biochemically independent signaling compartments. Thus, dynamic changes in the composition, distribution, mobility, conformations, and signaling properties of molecules contained within spines can account for much of the molecular basis of postsynaptic function and regulation. A major factor in controlling these changes is the diffusional properties of proteins within this small compartment. Advances in measurement techniques using fluorescence microscopy now make it possible to measure molecular diffusion within single dendritic spines directly. Here, we review the regulatory mechanisms of diffusion in spines by local intra-spine architecture and discuss their implications for neuronal signaling and synaptic plasticity.

Multidimensional Digital Bioassay Platform Based on an Air-Sealed Femtoliter Reactor Array Device.

Single-molecule experiments have been helping us to get deeper inside biological phenomena by illuminating how individual molecules actually work. Digital bioassay, in which analyte molecules are individually confined in small compartments to be analyzed, is an emerging technology in single-molecule biology and applies to various biological entities (e.g., cells and virus particles). However, digital bioassay is not compatible with multiconditional and multiparametric assays, hindering in-depth understanding of analytes. This is because current digital bioassay lacks a repeatable solution-exchange system that keeps analytes inside compartments. To address this challenge, we developed a digital bioassay platform with easy solution exchanges, called multidimensional (MD) digital bioassay. We immobilized single analytes in arrayed femtoliter (10-15 L) reactors and sealed them with airflow. The solution in each reactor was stable and showed no cross-talk via solution leakage for more than 2 h, and over 30 rounds of perfect solution exchanges were successfully performed. With multiconditional assays based on our system, we could quantitatively determine inhibitor sensitivities of single influenza A virus particles and single alkaline phosphatase (ALP) molecules, which has never been achieved with conventional digital bioassays. Further, we demonstrated that ALPs from two origins can be precisely distinguished by a single-molecule multiparametric assay with our system, which was also difficult with conventional digital bioassays. Thus, MD digital bioassay is a versatile platform to gain in-depth insight into biological entities in unprecedented resolution.

H2S sensing for breath analysis with Au functionalized ZnO nanowires

This work presents a H2S selective resistive gas sensor design based on a chemical field effect transistor (ChemFET) with open gate formed by hundreds of high temperature chemical vapour deposition (CVD) grown zinc oxide nanowires (ZnO NW). The sensing ability of pristine ZnO NWs and surface functionalized ZnO NWs for H2S is analysed systematically. ZnO NWs are functionalized by deposition of discontinuous gold (Au) nanoparticle films of different thicknesses of catalyst layer ranging from 1 to 10 nm and are compared in their gas sensing properties. All experiments were performed in a temperature stabilized small volume compartment with adjustable gas mixture at room temperature. The results allow for a well-founded understanding of signal-to-noise ratio, enhanced response, and improved limit of detection due to the Au functionalisation. Comprehension and controlled application of the beneficial effects of Au catalyst on ZnO NWs allow for the detection of very low H2S concentrations down to 10 ppb, and a theoretically estimated 500 ppt in synthetic air at room temperature.

Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation

ABSTRACT RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory formation. However, whether additional RNA modifications may be playing a role in neuronal functions and in response to environmental queues is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m2,2G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNAAla(AGC) isodecoders at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes may play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.

Burning dynamics and in-depth flame spread of wood cribs in large compartment fires

Wood cribs pervade the fire research literature as the chosen fuel load for testing within the built environment. As such, the underpinning knowledge of fire behaviour in compartments was developed from experiments using wood cribs in small compartments. Despite the apparent incomparability of porous fuel-beds such as cribs to real solid fuels in the built environment, the role of the fuel mass transfer number (“B-Number”) in defining the compartment fire dynamics has received little attention. In the case of large open-plan compartments, the burning processes are strongly dependant on the relationship of the fuel nature and compartment geometry. To address these limitations, the physical processes in-depth and external to a spreading wood crib fire in a compartment are examined. A theory to couple these processes to a compartment is proposed and analogised into the classical “Emmons problem”, leading to a definition of a total mass transfer number for a wood crib. Comparing the theory against data from a large-scale experiment shows that the wood crib approximates steady-state burning in two regimes: a fuel-bed-controlled regime and a momentum-controlled regime. The fuel-bed-controlled regime occurs when the burning and spread rates are governed by the processes internal to the crib, and the fire behaviour is therefore defined by the crib geometry. This regime is characterised by a fire that travels or grows slowly, with small external heat fluxes. The momentum-controlled regime occurs when the fire is fully-developed and the external heat fluxes are very large. Burning rates are controlled by the residence time, with the compartment fire dynamics defined by complex transport processes associated with the momentum-driven flows external to the crib. Transitions from the fuel-bed-controlled regime to the momentum-controlled regime are driven by accelerations in the flame spread rate along the surface of the crib leading to an additional energy input mechanism that is used to raise the in-depth flame spread rate of the crib. It is hypothesised that the burning mechanisms of fuels with large mass transfer numbers, such as non-charring plastics, diverge significantly from wood cribs, and therefore extrapolating test data from wood cribs fires in compartments to real fuels must be done with extreme caution. Thus, the nature of the fuel is an important and unavoidable consideration when studying the fire dynamics of large open-plan compartments.

CiliaQ: a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images

Cilia are hair-like membrane protrusions that emanate from the surface of most vertebrate cells and are classified into motile and primary cilia. Motile cilia move fluid flow or propel cells, while also fulfill sensory functions. Primary cilia are immotile and act as a cellular antenna, translating environmental cues into cellular responses. Ciliary dysfunction leads to severe diseases, commonly termed ciliopathies. The molecular details underlying ciliopathies and ciliary function are, however, not well understood. Since cilia are small subcellular compartments, imaging-based approaches have been used to study them. However, tools to comprehensively analyze images are lacking. Automatic analysis approaches require commercial software and are limited to 2D analysis and only a few parameters. The widely used manual analysis approaches are time consuming, user-biased, and difficult to compare. Here, we present CiliaQ, a package of open-source, freely available, and easy-to-use ImageJ plugins. CiliaQ allows high-throughput analysis of 2D and 3D, static or time-lapse images from fluorescence microscopy of cilia in cell culture or tissues, and outputs a comprehensive list of parameters for ciliary morphology, length, bending, orientation, and fluorescence intensity, making it broadly applicable. We envision CiliaQ as a resource and platform for reproducible and comprehensive analysis of ciliary function in health and disease.Graphic abstract

Synchrony and Oscillatory Dynamics for a 2-D PDE-ODE Model of Diffusion-Mediated Communication between Small Signaling Compartments

We analyze a class of cell-bulk coupled PDE-ODE models, motivated by quorum-sensing and diffusion-mediated behavior in microbial systems, that characterize communication between localized spatially...

Real-Time Monitoring and Detection of Emissions in Vehicles

This research aims to optimize the weight of already existing fire extinguishers containing Carbon Dioxide as per BIS standards IS 2190: 2010 and IS 7285-1: 2004. In the paper, an optimized and new design is proposed to minimize the weight of the pressure vessel making it easier to store in smaller compartments and also allowing faster hand-held use during an emergency. The weight has been reduced substantially by using proposed materials and FEA simulations were performed on the model to check for failures under the set test conditions with the aim to minimize the volume of metal used that is able to withstand the hydrostatic load of pressure gas. ANSYS Mechanical 18.2 was used for performing 3d pressure analysis while the model was designed on Solidworks 2016. A Multi Frontal Direct Solver was preferred to reach the solutions in every case. The analysis results of all the materials were compared and finally, a material was selected that was tough enough to clear the safety standards and extremely light so that even old people could use it without any issues. A simple shell of Titanium Grade-5 Alloy was found to be the proper and optimal choice to obtain good mechanical properties and lightweight.

Design and Analysis of Lightweight Fire Extinguishers using Alternately Available Metals

This research aims to optimize the weight of already existing fire extinguishers containing Carbon Dioxide as per BIS standards IS 2190: 2010 and IS 7285-1: 2004. In the paper, an optimized and new design is proposed to minimize the weight of the pressure vessel making it easier to store in smaller compartments and also allowing faster hand-held use during an emergency. The weight has been reduced substantially by using proposed materials and FEA simulations were performed on the model to check for failures under the set test conditions with the aim to minimize the volume of metal used that is able to withstand the hydrostatic load of pressure gas. ANSYS Mechanical 18.2 was used for performing 3d pressure analysis while the model was designed on Solidworks 2016. A Multi Frontal Direct Solver was preferred to reach the solutions in every case. The analysis results of all the materials were compared and finally, a material was selected that was tough enough to clear the safety standards and extremely light so that even old people could use it without any issues. A simple shell of Titanium Grade-5 Alloy was found to be the proper and optimal choice to obtain good mechanical properties and lightweight.

Artificial Biosystems by Printing Biology.

The continuous progress of printing technologies over the past 20 years has fueled the development of a plethora of applications in materials sciences, flexible electronics, and biotechnologies. More recently, printing methodologies have started up to explore the world of Artificial Biology, offering new paradigms in the direct assembly of Artificial Biosystems (small condensates, compartments, networks, tissues, and organs) by mimicking the result of the evolution of living systems and also by redesigning natural biological systems, taking inspiration from them. This recent progress is reported in terms of a new field here defined as Printing Biology, resulting from the intersection between the field of printing and the bottom up Synthetic Biology. Printing Biology explores new approaches for the reconfigurable assembly of designed life-like or life-inspired structures. This work presents this emerging field, highlighting its main features, i.e., printing methodologies (from 2D to 3D), molecular ink properties, deposition mechanisms, and finally the applications and future challenges. Printing Biology is expected to show a growing impact on the development of biotechnology and life-inspired fabrication.

Novel model of restricted mobility induced osteopenia in zebrafish.

Immobilization, such as prolonged bed rest, is a risk factor for bone loss in humans. Motivated by the emerging utility of zebrafish (Danio rerio) as an animal of choice for the study of musculoskeletal disease, here we report a model of restricted mobility induced osteopenia in adult zebrafish. Aquatic tanks with small cubical compartments to restrict the movement and locomotion of single fish were designed and fabricated for this study. Adult zebrafish were divided into two groups: a normal control (CONT) and a restricted mobility group (RMG) (18 fish/group). Six fish from each group were euthanized on days 14, 21 and 35 of the movement restriction. By using microcomputed tomography (micro-CT), we assessed bone volume/tissue volume (BV/TV) and bone density in the whole skeleton of the fish. Furthermore, we assessed skeletal shape in the vertebrae (radius, length, volume, neural and haemal arch aperture areas, neural and haemal arch angle, and thickness of the intervertebral space), single vertebra bone volume and bone density. Movement restriction significantly decreased vertebral skeletal parameters such as radius, length, volume, arch aperture areas and angles as well as the thickness of the intervertebral space in RMG. Furthermore, restricted mobility significantly (P < 0.001) decreased BV/TV and bone density as compared to the CONT group, starting as early as 14 days. By analysing zebrafish from CONT and RMG, we show that micro-CT imaging is a sensitive method to quantify distinct skeletal properties in zebrafish. We further defined the micro-CT parameters which can be used to examine the effects of restricted mobility on the skeleton of the fish. Our findings propose a rapid and effective osteopenia "stabulation" model, which could be used widely for osteoporosis drug screening.

On the solution of the traumatic avoidance learning model approached by the Banach fixed point theorem

This paper deals with a specific type of traumatic avoidance for the learning process of normal dogs enclosed into a small compartment with a steel grid floor. Our aim is to analyze the behavior of the dogs in such situations and to construct a suitable mathematical model for it. The existence and uniqueness results of the proposed traumatic avoidance learning model are being investigated by the use of the Banach fixed point theorem.