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Acquisition of ephemeral module in roots: a new view and test.

ABSTRACT: The terminal root branch orders composed mainly of primarily-developed tissues are increasingly recognized as an ephemeral module specialized for resource absorption. This root module is crucial in driving a range of ecosystem processes such as belowground productivity, carbon and nutrient cycling. Traditionally, acquisition of the ephemeral root module is achieved by separating these primarily-developed branch orders with forceps. However, obtaining this root segment with forceps approach is labor-intensive which may not be applicable for studies with an appreciable amount of root samples. To address this challenge, we developed a new idea to obtain the ephemeral root module. In this new view, root samples were tenderly kneaded by hand and the detached roots are considered as the ephemeral root module. To test this idea, four species with contrasting growing environment were selected and a range of chemicals were determined including C, N, P, Ca, S, Mg, Ba, Zn, Mn, Pb, Cu, V and Li. We found no or little difference of these chemicals in roots by hand-kneading approach from roots by forceps approach. These results suggested that hand-kneading method could be a convenient way to acquire ephemeral root module.

SUBMITTER: Kong D

PROVIDER: S-EPMC4035572 | biostudies-other | 2014

REPOSITORIES: biostudies-other

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| PRJEB45440 | ENA

Structure learning and the Occam's razor principle: a new view of human function acquisition.

Project description:We often encounter pairs of variables in the world whose mutual relationship can be described by a function. After training, human responses closely correspond to these functional relationships. Here we study how humans predict unobserved segments of a function that they have been trained on and we compare how human predictions differ to those made by various function-learning models in the literature. Participants' performance was best predicted by the polynomial functions that generated the observations. Further, participants were able to explicitly report the correct generating function in most cases upon a post-experiment survey. This suggests that humans can abstract functions. To understand how they do so, we modeled human learning using an hierarchical Bayesian framework organized at two levels of abstraction: function learning and parameter learning, and used it to understand the time course of participants' learning as we surreptitiously changed the generating function over time. This Bayesian model selection framework allowed us to analyze the time course of function learning and parameter learning in relative isolation. We found that participants acquired new functions as they changed and even when parameter learning was not completely accurate, the probability that the correct function was learned remained high. Most importantly, we found that humans selected the simplest-fitting function with the highest probability and that they acquired simpler functions faster than more complex ones. Both aspects of this behavior, extent and rate of selection, present evidence that human function learning obeys the Occam's razor principle.

| S-EPMC4179744 | biostudies-literature

ABE-VIEW: Android Interface for Wireless Data Acquisition and Control.

Project description:Advances in scientific knowledge are increasingly supported by a growing community of developers freely sharing new hardware and software tools. In this spirit we have developed a free Android app, ABE-VIEW, that provides a flexible graphical user interface (GUI) populated entirely from a remote instrument by ascii-coded instructions communicated wirelessly over Bluetooth. Options include an interactive chart for plotting data in real time, up to 16 data fields, and virtual controls including buttons, numerical controls with user-defined range and resolution, and radio buttons which the user can use to send coded instructions back to the instrument. Data can be recorded into comma delimited files interactively at the user's discretion. Our original objective of the project was to make data acquisition and control for undergraduate engineering labs more modular and affordable, but we have also found that the tool is highly useful for rapidly testing novel sensor systems for iterative improvement. Here we document the operation of the app and syntax for communicating with it. We also illustrate its application in undergraduate engineering labs on dynamic systems modeling, as well as for identifying the source of harmonic distortion affecting electrochemical impedance measurements at certain frequencies in a novel wireless potentiostat.

| S-EPMC6111993 | biostudies-literature

Reliability test of the QC module in DeepRTAlign

Project description:Micro-flow LC-MS/MS analysis of pure 293T or E.coli.

2023-07-31 | PXD044223 |

A Femoral Tunnel View Test During ACL Reconstruction.

Project description:Despite technologic advances in the surgical techniques for anterior cruciate ligament (ACL) reconstruction, some patients continue to have violation of the femoral cortex, commonly referred to as wall blowout. These posterior or lateral cortical breaches lead to loss of graft containment and subsequent difficulty with graft fixation. If this intraoperative error is not promptly recognized and treated, the graft is at an increased risk of premature failure. Thus, in these situations, recognizing the complication and knowing strategies for alternative or salvage fixation are of importance. This article details a simple tunnel view test realized during ACL reconstruction that would enable determining the integrity and depth of the femoral tunnel. The femoral tunnel view test is a technically straightforward and quick test able to obtain a superior view of patient anatomy to facilitate accurate tunnel integrity evaluation during ACL reconstruction.

| S-EPMC5621967 | biostudies-literature

SCHENGEN receptor module drives localized ROS production and lignification in plant roots.

Project description:Production of reactive oxygen species (ROS) by NADPH oxidases (NOXs) impacts many processes in animals and plants, and many plant receptor pathways involve rapid, NOX-dependent increases of ROS. Yet, their general reactivity has made it challenging to pinpoint the precise role and immediate molecular action of ROS. A well-understood ROS action in plants is to provide the co-substrate for lignin peroxidases in the cell wall. Lignin can be deposited with exquisite spatial control, but the underlying mechanisms have remained elusive. Here, we establish a kinase signaling relay that exerts direct, spatial control over ROS production and lignification within the cell wall. We show that polar localization of a single kinase component is crucial for pathway function. Our data indicate that an intersection of more broadly localized components allows for micrometer-scale precision of lignification and that this system is triggered through initiation of ROS production as a critical peroxidase co-substrate.

| S-EPMC7196915 | biostudies-literature

Global view of the RAF-MEK-ERK module and its immediate downstream effectors.

Project description:Small molecule inhibitors of BRAF and MEK have proven effective at inhibiting tumor growth in melanoma patients, however this efficacy is limited due to the almost universal development of drug resistance. To provide advanced insight into the signaling responses that occur following kinase inhibition we have performed quantitative (phospho)-proteomics of human melanoma cells treated with either dabrafenib, a BRAF inhibitor; trametinib, a MEK inhibitor or SCH772984, an ERK inhibitor. Over nine experiments we identified 7827 class I phosphorylation sites on 4960 proteins. This included 54 phosphorylation sites that were significantly down-modulated after exposure to all three inhibitors, 34 of which have not been previously reported. Functional analysis of these novel ERK targets identified roles for them in GTPase activity and regulation, apoptosis and cell-cell adhesion. Comparison of the results presented here with previously reported phosphorylation sites downstream of ERK showed a limited degree of overlap suggesting that ERK signaling responses may be highly cell line and cue specific. In addition we identified 26 phosphorylation sites that were only responsive to dabrafenib. We provide further orthogonal experimental evidence for 3 of these sites in human embryonic kidney cells over-expressing BRAF as well as further computational insights using KinomeXplorer. The validated phosphorylation sites were found to be involved in actin regulation, which has been proposed as a novel mechanism for inhibiting resistance development. These results would suggest that the linearity of the BRAF-MEK-ERK module is at least context dependent.

| S-EPMC6659682 | biostudies-literature

The AIDSS Module for Data Acquisition in Crisis Situations and Environmental Protection.

Project description:The Toolbox implementation for removal of antipersonnel mines, submunitions and unexploded ordnance (TIRAMISU) Advanced Intelligence Decision Support System is an operational system proposed to Mine Action Centres worldwide for conducting non-technical surveys in humanitarian demining. The system consists of three modules, one of which is the module for data acquisition introduced and described in this study. The module has been designed, produced, improved, used and operationally tested and validated on several platforms (helicopters, remotely piloted aircraft systems (RPAS) and a blimp), with various sensors and acquisition units (Global Positioning System (GPS) and inertial measurement unit) in a variety of combinations for additional data acquisition from deep inside a suspected hazardous area. For the purposes of aerial data acquisition over a suspected hazardous area, the use of multiple sensors such as visible digital cameras and multi-spectral visible, near infrared (VNIR), hyperspectral VNIR and thermal infrared sensors are of benefit, because they display the scene in different ways. Off-the-shelf equipment and software were mostly used, but some specific equipment, such as sensor pods, was developed and also some software solutions for data acquisition and pre-processing (transforming hyperspectral line scanner data into hyperspectral images, and producing hyperspectral cubes). The technical stability and robustness of the module were confirmed by operationally testing and evaluating the systems on the aforementioned platforms and missions in several actual suspected hazardous areas in Croatia and Bosnia and Herzegovina, between 2001 and 2015.

| S-EPMC7085737 | biostudies-literature

Mechanisms of spacer acquisition by sequential assembly of the adaptation module in Synechocystis.

Project description:CRISPR-Cas immune systems process and integrate short fragments of DNA from new invaders as spacers into the host CRISPR locus to establish molecular memory of prior infection, which is also known as adaptation in the field. Some CRISPR-Cas systems rely on Cas1 and Cas2 to complete the adaptation process, which has been characterized in a few systems. In contrast, many other CRISPR-Cas systems require an additional factor of Cas4 for efficient adaptation, the mechanism of which remains less understood. Here we present biochemical reconstitution of the Synechocystis sp. PCC6803 type I-D adaptation system, X-ray crystal structures of Cas1-Cas2-prespacer complexes, and negative stained electron microscopy structure of the Cas4-Cas1 complex. Cas4 and Cas2 compete with each other to interact with Cas1. In the absence of prespacer, Cas4 but not Cas2 assembles with Cas1 into a very stable complex for processing the prespacer. Strikingly, the Cas1-prespacer complex develops a higher binding affinity toward Cas2 to form the Cas1-Cas2-prespacer ternary complex for integration. Together, we show a two-step sequential assembly mechanism for the type I-D adaptation module of Synechocystis, in which Cas4-Cas1 and Cas1-Cas2 function as two exclusive complexes for prespacer processing, capture, and integration.

| S-EPMC7969031 | biostudies-literature

A YAP/TAZ-TEAD signalling module links endothelial nutrient acquisition to angiogenic growth.

Project description:Angiogenesis, the process by which endothelial cells (ECs) form new blood vessels from existing ones, is intimately linked to the tissue's metabolic milieu and often occurs at nutrient-deficient sites. However, ECs rely on sufficient metabolic resources to support growth and proliferation. How endothelial nutrient acquisition and usage are regulated is unknown. Here we show that these processes are instructed by Yes-associated protein 1 (YAP)/WW domain-containing transcription regulator 1 (WWTR1/TAZ)-transcriptional enhanced associate domain (TEAD): a transcriptional module whose function is highly responsive to changes in the tissue environment. ECs lacking YAP/TAZ or their transcriptional partners, TEAD1, 2 and 4 fail to divide, resulting in stunted vascular growth in mice. Conversely, activation of TAZ, the more abundant paralogue in ECs, boosts proliferation, leading to vascular hyperplasia. We find that YAP/TAZ promote angiogenesis by fuelling nutrient-dependent mTORC1 signalling. By orchestrating the transcription of a repertoire of cell-surface transporters, including the large neutral amino acid transporter SLC7A5, YAP/TAZ-TEAD stimulate the import of amino acids and other essential nutrients, thereby enabling mTORC1 activation. Dissociating mTORC1 from these nutrient inputs-elicited by the loss of Rag GTPases-inhibits mTORC1 activity and prevents YAP/TAZ-dependent vascular growth. Together, these findings define a pivotal role for YAP/TAZ-TEAD in controlling endothelial mTORC1 and illustrate the essentiality of coordinated nutrient fluxes in the vasculature.

| S-EPMC9236904 | biostudies-literature

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