-
Current Biology : CB Nov 2019The radiation of life on Earth was accompanied by the diversification of multicellular body plans in the eukaryotic kingdoms Animalia, Plantae, Fungi and Chromista.... (Review)
Review
The radiation of life on Earth was accompanied by the diversification of multicellular body plans in the eukaryotic kingdoms Animalia, Plantae, Fungi and Chromista. Branching forms are ubiquitous in nature and evolved repeatedly in the above lineages. The developmental and genetic basis of branch formation is well studied in the three-dimensional shoot and root systems of land plants, and in animal organs such as the lung, kidney, mammary gland, vasculature, etc. Notably, recent thought-provoking studies combining experimental analysis and computational modeling of branching patterns in whole animal organs have identified global patterning rules and proposed unifying principles of branching morphogenesis. Filamentous branching forms represent one of the simplest expressions of the multicellular body plan and constitute a key step in the evolution of morphological complexity. Similarities between simple and complex branching forms distantly related in evolution are compelling, raising the question whether shared mechanisms underlie their development. Here, we focus on filamentous branching organisms that represent major study models from three distinct eukaryotic kingdoms, including the moss Physcomitrella patens (Plantae), the brown alga Ectocarpus sp. (Chromista), and the ascomycetes Neurospora crassa and Aspergillus nidulans (Fungi), and bring to light developmental regulatory mechanisms and design principles common to these lineages. Throughout the review we explore how the regulatory mechanisms of branching morphogenesis identified in other models, and in particular animal organs, may inform our thinking on filamentous systems and thereby advance our understanding of the diverse strategies deployed across the eukaryotic tree of life to evolve similar forms.
Topics: Ascomycota; Body Patterning; Bryopsida; Phaeophyceae
PubMed: 31689405
DOI: 10.1016/j.cub.2019.09.021 -
International Journal of Molecular... Jan 2021Rice grain yield is a complex trait determined by three components: panicle number, grain number per panicle (GNPP) and grain weight. GNPP is the major contributor to... (Review)
Review
Rice grain yield is a complex trait determined by three components: panicle number, grain number per panicle (GNPP) and grain weight. GNPP is the major contributor to grain yield and is crucial for its improvement. GNPP is determined by a series of physiological and biochemical steps, including inflorescence development, formation of rachis branches such as primary rachis branches and secondary rachis branches, and spikelet specialisation (lateral and terminal spikelets). The molecular genetic basis of GNPP determination is complex, and it is regulated by numerous interlinked genes. In this review, panicle development and the determination of GNPP is described briefly, and GNPP-related genes that influence its determination are categorised according to their regulatory mechanisms. We introduce genes related to rachis branch development and their regulation of GNPP, genes related to phase transition (from rachis branch meristem to spikelet meristem) and their regulation of GNPP, and genes related to spikelet specialisation and their regulation of GNPP. In addition, we describe other GNPP-related genes and their regulation of GNPP. Research on GNPP determination suggests that it is possible to cultivate rice varieties with higher grain yield by modifying GNPP-related genes.
Topics: Edible Grain; Gene Expression Regulation, Plant; Genes, Plant; Genetic Association Studies; Oryza; Plant Development; Quantitative Trait, Heritable
PubMed: 33450933
DOI: 10.3390/ijms22020728 -
Frontiers in Medical Technology 2022Nanoparticles (NP) are being increasingly explored as vehicles for targeted drug delivery because they can overcome free therapeutic limitations by drug encapsulation,...
Nanoparticles (NP) are being increasingly explored as vehicles for targeted drug delivery because they can overcome free therapeutic limitations by drug encapsulation, thereby increasing solubility and transport across cell membranes. However, a translational gap exists from animal to human studies resulting in only several NP having FDA approval. Because of this, researchers have begun to turn toward physiologically based pharmacokinetic (PBPK) models to guide NP experimentation. However, typical PBPK models use an empirically derived framework that cannot be universally applied to varying NP constructs and experimental settings. The purpose of this study was to develop a physics-based multiscale PBPK compartmental model for determining continuous NP biodistribution. We successfully developed two versions of a physics-based compartmental model, models A and B, and validated the models with experimental data. The more physiologically relevant model (model B) had an output that more closely resembled experimental data as determined by normalized root mean squared deviation (NRMSD) analysis. A branched model was developed to enable the model to account for varying NP sizes. With the help of the branched model, we were able to show that branching in vasculature causes enhanced uptake of NP in the organ tissue. The models were solved using two of the most popular computational platforms, MATLAB and Julia. Our experimentation with the two suggests the highly optimized ODE solver package DifferentialEquations.jl in Julia outperforms MATLAB when solving a stiff system of ordinary differential equations (ODEs). We experimented with solving our PBPK model with a neural network using Julia's Flux.jl package. We were able to demonstrate that a neural network can learn to solve a system of ODEs when the system can be made non-stiff quasi-steady-state approximation (QSSA). Our model incorporates modules that account for varying NP surface chemistries, multiscale vascular hydrodynamic effects, and effects of the immune system to create a more comprehensive and modular model for predicting NP biodistribution in a variety of NP constructs.
PubMed: 35909883
DOI: 10.3389/fmedt.2022.934015 -
Genes Mar 2021Minimum free energy prediction of RNA secondary structures is based on the Nearest Neighbor Thermodynamics Model. While such predictions are typically good, the accuracy...
Minimum free energy prediction of RNA secondary structures is based on the Nearest Neighbor Thermodynamics Model. While such predictions are typically good, the accuracy can vary widely even for short sequences, and the branching thermodynamics are an important factor in this variance. Recently, the simplest model for multiloop energetics-a linear function of the number of branches and unpaired nucleotides-was found to be the best. Subsequently, a parametric analysis demonstrated that per family accuracy can be improved by changing the weightings in this linear function. However, the extent of improvement was not known due to the ad hoc method used to find the new parameters. Here we develop a branch-and-bound algorithm that finds the set of optimal parameters with the highest average accuracy for a given set of sequences. Our analysis shows that the previous ad hoc parameters are nearly optimal for tRNA and 5S rRNA sequences on both training and testing sets. Moreover, cross-family improvement is possible but more difficult because competing parameter regions favor different families. The results also indicate that restricting the unpaired nucleotide penalty to small values is warranted. This reduction makes analyzing longer sequences using the present techniques more feasible.
Topics: Algorithms; Entropy; Humans; Nucleic Acid Conformation; RNA; RNA, Ribosomal, 5S; RNA, Transfer; Thermodynamics
PubMed: 33805944
DOI: 10.3390/genes12040469 -
Developmental Biology Jul 2019Dendrites are the input compartment of the neuron, receiving and integrating incoming information. Dendritic trees are often highly complex and branched. Their branch... (Review)
Review
Dendrites are the input compartment of the neuron, receiving and integrating incoming information. Dendritic trees are often highly complex and branched. Their branch extension and distribution are tightly correlated with their role and interactions within neuronal networks. Thus, intense research has focused on understanding the mechanisms that govern dendrite elaboration. Recent reports highlight the importance of specific lipids for these processes. In particular, glycerophospholipids and several of their interacting proteins are involved in various steps of dendrite growth, including the initiation and elongation of dendritic branches and dendritic spines. The aim of this review is to provide a general overview about which particular lipids are involved in shaping dendrite morphology during neuronal differentiation. Additionally, it summarizes recent studies, which helped to gain insights into the mechanisms by which glycerophospholipids and their associated proteins contribute to establishing correct dendritic morphologies.
Topics: Animals; Cell Differentiation; Dendritic Spines; Glycerophospholipids; Humans
PubMed: 30576627
DOI: 10.1016/j.ydbio.2018.12.009 -
Journal of Taibah University Medical... Oct 2020This study examined variations in the termination level of the radial nerve (RN) and the morphometry of the RN and its branches at potential compression sites....
OBJECTIVES
This study examined variations in the termination level of the radial nerve (RN) and the morphometry of the RN and its branches at potential compression sites. Additionally, we digitally analysed histological sections of the RN, the superficial branch of the radial nerve (SBRN), and the posterior interosseous nerve (PIN).
METHODS
We conducted this study on 14 formalin fixed adult cadavers. The lengths of the RN, SBRN, and PIN were measured up to potential compression sites, using appropriate surface skeletal landmarks as reference points. We histologically evaluated the fascicular and non-fascicular areas and the number of axons in each nerve. All parameters were statistically analysed using a paired t-test.
RESULTS
We found variations in the bifurcation of the RN with respect to the biepicondylar line (BEL). However, the course of RN terminal branches was constant in the forearm. There was a significant histological difference between the fascicular and non-fascicular areas of the PIN. There was no significant difference in the total number of axons in the SBRN and PIN. Finally, we observed that the intramuscular length of the PIN within the supinator muscle was variable and that the SBRN had more fascicles compared to the RN and PIN.
CONCLUSIONS
In our study, the RN and PIN had more variable morphometry compared to that of the SBRN. The histologic evaluation and quantification of these nerves at their potential compression sites could serve as a guide for surgeons planning nerve reconstruction procedures.
PubMed: 33132807
DOI: 10.1016/j.jtumed.2020.07.009 -
Revista Brasileira de Ortopedia Oct 2020To perform an anatomical study of the location of the infrapatellar branch of the saphenous nerve in relation to the structures of the knee. An anatomical study...
To perform an anatomical study of the location of the infrapatellar branch of the saphenous nerve in relation to the structures of the knee. An anatomical study was performed by dissection of 18 humans knees (9 right and 9 left knees). After exposure of the infrapatellar branch and its direct and indirect branches, they were then measured. We adopted a quadrant in the medial region of the knee delimited by two transversal planes as a parameter of the study. In 17 of the 18 knees (94.4%) studied, a single infrapatellar branch was observed. The infrapatellar branch emerged as fibers of the womb of the sartorius muscle in 17 of the 18 knees (94.4%). In relation to the branch, we observed that in 100% of the knees the infrapatellar branch had at least one primary branch, resulting in a superior branch and an inferior branch. In 9 limbs (50% of the cases) this branch occurred outside the proposed quadrant, and, in the remaining limbs, it occurred within the quadrant. The infrapatellar saphenous nerve branch was found in all dissected knees, and, in 94.4% of the cases, it was of the penetrating type; in 100% of the cases, it originated two primary direct branches. The direct and indirect branches presented great variability regarding their path.
PubMed: 33093719
DOI: 10.1055/s-0040-1701287 -
Biochemical Society Transactions Feb 2024The Arp2/3 complex, which generates both branched but also linear actin filaments via activation of SPIN90, is evolutionarily conserved in eukaryotes. Several factors... (Review)
Review
The Arp2/3 complex, which generates both branched but also linear actin filaments via activation of SPIN90, is evolutionarily conserved in eukaryotes. Several factors regulate the stability of filaments generated by the Arp2/3 complex to maintain the dynamics and architecture of actin networks. In this review, we summarise recent studies on the molecular mechanisms governing the tuning of Arp2/3 complex nucleated actin filaments, which includes investigations using microfluidics and single-molecule imaging to reveal the mechanosensitivity, dissociation and regeneration of actin branches. We also discuss the high-resolution cryo-EM structure of cortactin bound to actin branches, as well as the differences and similarities between the stability of Arp2/3 complex nucleated branches and linear filaments. These new studies provide a clearer picture of the stabilisation of Arp2/3 nucleated filaments at the molecular level. We also identified gaps in our understanding of how different factors collectively contribute to the stabilisation of Arp2/3 complex-generated actin networks.
Topics: Actin-Related Protein 2-3 Complex; Actins; Actin Cytoskeleton; Cytoskeleton
PubMed: 38288872
DOI: 10.1042/BST20230638 -
World Journal of Surgical Oncology Feb 2023Laparoscopic and robotic surgery for transverse colon cancer are difficult due to complex fusion of the foregut and midgut and variation of the vessels of the transverse...
BACKGROUND
Laparoscopic and robotic surgery for transverse colon cancer are difficult due to complex fusion of the foregut and midgut and variation of the vessels of the transverse colon. Although the vessels of the right colon have been investigated, middle colic artery (MCA) variation and the relationship with vessels around the transvers colon are unknown. We investigated variation of the MCA using computed tomography angiography (CTA) and cadaver specimen and the relationship between the superior mesenteric vein (SMV) and MCA using CTA. The classification of vessels around the transverse colon may lead to safer and reliable surgery.
METHODS
This study included 505 consecutive patients who underwent CTA in our institution from 2014 to 2020 and 44 cadaver specimens. Vascular anatomical classifications and relationships were analyzed using CT images.
RESULTS
The MCA was defined as the arteries arising from the superior mesenteric artery (SMA) that flowed into the transverse colon at the distal ends. The classifications were as follows: type I, branching right and left from common trunk; type II, the right and left branches bifurcated separately from the SMA; and type III, the MCA branched from a vessel other than the SMA. Type II was subclassified into two subtypes, type IIa with one left branch and type IIb with two or more left branches from SMA. In the CTA and cadaver studies, respectively, the classifications were as follows: type I, n = 290 and n = 31; type IIa, n = 211 and n = 13; type IIb, n = 3 and n = 0; and type III, n = 1 and n = 0. We classified the relationship between the MCA and left side of the SMV into three types: type A, a common trunk runs along the left edge of the SMV (n = 173; 59.7%); type B, a right branch of the MCA runs along the left edge of the SMV (n = 116; 40.0%); and type C, the MCA runs dorsal of the SMV (n = 1; 0.3%).
CONCLUSIONS
This study revealed that The MCA branching classifications and relationship between the SMV and MCA. Preoperative CT angiography may be able to reliably identify vessel variation, which may be useful in clinical practice.
Topics: Humans; Colon, Transverse; Computed Tomography Angiography; Colon; Colonic Neoplasms; Mesentery; Laparoscopy; Cadaver
PubMed: 36747176
DOI: 10.1186/s12957-023-02919-9