Monte Carlo Method with Heuristic Adjustment for Irregularly Shaped Food Product Volume Measurement

Volume measurement plays an important role in the production and processing of food products. Various methods have been proposed to measure the volume of food products with irregular shapes based on 3D reconstruction. However, 3D reconstruction comes with a high-priced computational cost. Furthermore, some of the volume measurement methods based on 3D reconstruction have a low accuracy. Another method for measuring volume of objects uses Monte Carlo method. Monte Carlo method performs volume measurements using random points. Monte Carlo method only requires information regarding whether random points fall inside or outside an object and does not require a 3D reconstruction. This paper proposes volume measurement using a computer vision system for irregularly shaped food products without 3D reconstruction based on Monte Carlo method with heuristic adjustment. Five images of food product were captured using five cameras and processed to produce binary images. Monte Carlo integration with heuristic adjustment was performed to measure the volume based on the information extracted from binary images. The experimental results show that the proposed method provided high accuracy and precision compared to the water displacement method. In addition, the proposed method is more accurate and faster than the space carving method

A Dance with Protein Assemblies : Analysis, Structure Prediction, and Design

Protein assemblies are some of the most complex molecular machines in nature. They facilitate many cellular functions, from DNA replication to molecular motion, energy production, and even the production of other proteins. In a series of 3 papers, we analyzed the structure, developed structure prediction tools, and design tools, for different protein assemblies. Many of the studies were centered around viral protein capsids. Viral capsids are protein coats found inside viruses that contain and protect the viral genome. In one paper, we studied the interfaces of these capids and their energy landscapes. We found that they differ from regular homomers in terms of the amino acid composition and size, but not in the quality of interactions. This contradicts existing experimental and theoretical studies that suggest that the interactions are weak. We hypothesise that the occlusion by our models of electrostatic and entropic contributions might be at play. In another paper, we developed methods to predict large cubic symmetrical protein assemblies, such as viral capsids, from sequence. This method is based upon AlphaFold, a new AI tool that has revolutionized protein structure prediction. We found that we can predict up to 50% of the structures of these assemblies. The method can quickly elucidate the structure of many relevant proteins for humans, and for understanding structures relevant to disease, such as the structures of viral capsids. In the final paper, we developed tools to design capsid-like proteins called cages – structures that can be used for drug delivery and vaccine design. A fundamental problem in designing cage structures is achieving different architectures and low porosity, goals that are important for vaccine design and the delivery of small drug molecules. By explicitly modelling the shapes of the subunits in the cage and matching the shapes with proteins from structural databases, we find that we can create structures with many different sizes, shapes, and porosities - including low porosities. While waiting for experimental validation, the design strategy described in the paper must be extended, and more designs must be tested

Regulatory mechanisms and biological implications of protein complex assembly

Every living organism possesses a genome that contains within it a unique set of genes, a substantial number of which encode proteins. Over the last 20 years, it has become apparent that organismal complexity arises not from the specific complement of genes per se, but rather from interactions between the gene products - in particular, interactions between proteins. As an inevitable consequence of the crowded cellular interior, most protein-protein interactions are fleeting. However, many are significantly more long-lived and result in stable protein complexes, in which the constituent subunits are obligately dependent on their binding partners. Despite the abundance of protein complexes and their critical importance to the cell, we currently have an incomplete understanding of the mechanisms by which the cell ensures their correct assembly. In the chapters that follow, I have attempted to improve our understanding of the regulatory systems underlying assembly of protein complexes, and the way in which assembly as a whole affects the behaviour of the cell. The thesis opens with an extended literature review covering the currently available methods for characterising protein complexes. After this introduction, chapters 2-4 are concerned with regulatory mechanisms and biological implications common to the assembly of all protein complexes. Chapter 5 diverges from this work, and describes a family of evolutionarily related proteins that regulate the behaviour of condensins and cohesins. Bacterial and archaeal genomes contain far less non-coding DNA than eukaryotes, and coding genes are often packaged into discrete units known as operons. The proteins encoded within operons are usually functionally related, either through participation in metabolic pathways or as subunits of heteromeric protein complexes. Since protein complexes assemble via ordered pathways, we reasoned that there might be a signature of assembly order present in operons, the genes of which are translated in sequential order. By comparing computationally predicted assembly pathways with gene order in operons, we demonstrated this to be the case for the large majority of operon-encoded complexes. Within operons, gene order follows assembly order, and adjacent genes are substantially more likely to share a physical interface than those further apart. This work demonstrates that efficient assembly of complexes is of sufficient importance as to have placed major constraints on the evolution of operon gene order. Following this study of bacterial operons, I present results from research investigating how patterns of protein degradation in eukaryotes are influenced by the formation of protein complexes. This showed that, whilst most proteins display exponential degradation kinetics, a sizeable minority deviate considerably from this pattern, instead being more consistent with a two-step degradation process. These proteins are predominantly members of heteromeric complexes, and their two-step decay profiles can be explained using a model under which bound and unbound subunits are degraded at different rates. Within individual complexes, we find that non-exponentially decaying proteins tend to form larger interfaces, assemble earlier, and show a higher degree of coexpression, consistent with the idea that bound subunits are degraded at a slower rate than unbound or peripheral subunits. This model also explains the behaviour of proteins in aneuploid cells where one or more chromosomes have been duplicated. In general, protein abundance scales with gene copy number, so that the immediate effect of duplicating a chromosome is to double the abundance of the proteins encoded on it. However, previous analyses of mass spectrometry data, as well as my own, have shown that the abundance of many proteins on duplicated chromosomes is significantly attenuated compared to what one would expect. These proteins, like those with non-exponential degradation patterns, are very often members of larger complexes. Since the overall concentration of a protein complex is constrained by that of its least abundant members, duplicating a single subunit will predominantly increase the unbound, unstable fraction of that subunit. The results from this work strongly suggest that the apparent attenuation of many proteins observed in aneuploid cells is indeed a consequence of the failure of these proteins to assemble into complexes. Finally, I present a study concerning an important, universally conserved family of protein complexes, namely the SMC-kleisins. Two members of this family, condensin and cohesin, are responsible for two hallmarks of eukaryotic chromatin organisation: the formation of condensed, linear chromosomes, and sister chromatid cohesion during cell division. Unlike other SMC-kleisins, condensin and cohesin possess a number of regulators containing HEAT repeats. By developing a computational pipeline for searching and clustering paralogous repeat proteins, I was able to demonstrate that these regulators form a distinct sub-family within the larger class of HEAT repeat proteins. Furthermore, these regulators arose very early in eukaryotic history, hinting at a possible role in the origin of modern condensins and cohesins

Dynamics of Macrosystems; Proceedings of a Workshop, September 3-7, 1984

There is an increasing awareness of the important and persuasive role that instability and random, chaotic motion play in the dynamics of macrosystems. Further research in the field should aim at providing useful tools, and therefore the motivation should come from important questions arising in specific macrosystems. Such systems include biochemical networks, genetic mechanisms, biological communities, neutral networks, cognitive processes and economic structures. This list may seem heterogeneous, but there are similarities between evolution in the different fields. It is not surprising that mathematical methods devised in one field can also be used to describe the dynamics of another. IIASA is attempting to make progress in this direction. With this aim in view this workshop was held at Laxenburg over the period 3-7 September 1984. These Proceedings cover a broad canvas, ranging from specific biological and economic problems to general aspects of dynamical systems and evolutionary theory

Remote Sensing of Plant Biodiversity

At last, here it is. For some time now, the world has needed a text providing both a new theoretical foundation and practical guidance on how to approach the challenge of biodiversity decline in the Anthropocene. This is a global challenge demanding global approaches to understand its scope and implications. Until recently, we have simply lacked the tools to do so. We are now entering an era in which we can realistically begin to understand and monitor the multidimensional phenomenon of biodiversity at a planetary scale. This era builds upon three centuries of scientific research on biodiversity at site to landscape levels, augmented over the past two decades by airborne research platforms carrying spectrometers, lidars, and radars for larger-scale observations. Emerging international networks of fine-grain in-situ biodiversity observations complemented by space-based sensors offering coarser-grain imagery—but global coverage—of ecosystem composition, function, and structure together provide the information necessary to monitor and track change in biodiversity globally. This book is a road map on how to observe and interpret terrestrial biodiversity across scales through plants—primary producers and the foundation of the trophic pyramid. It honors the fact that biodiversity exists across different dimensions, including both phylogenetic and functional. Then, it relates these aspects of biodiversity to another dimension, the spectral diversity captured by remote sensing instruments operating at scales from leaf to canopy to biome. The biodiversity community has needed a Rosetta Stone to translate between the language of satellite remote sensing and its resulting spectral diversity and the languages of those exploring the phylogenetic diversity and functional trait diversity of life on Earth. By assembling the vital translation, this volume has globalized our ability to track biodiversity state and change. Thus, a global problem meets a key component of the global solution. The editors have cleverly built the book in three parts. Part 1 addresses the theory behind the remote sensing of terrestrial plant biodiversity: why spectral diversity relates to plant functional traits and phylogenetic diversity. Starting with first principles, it connects plant biochemistry, physiology, and macroecology to remotely sensed spectra and explores the processes behind the patterns we observe. Examples from the field demonstrate the rising synthesis of multiple disciplines to create a new cross-spatial and spectral science of biodiversity. Part 2 discusses how to implement this evolving science. It focuses on the plethora of novel in-situ, airborne, and spaceborne Earth observation tools currently and soon to be available while also incorporating the ways of actually making biodiversity measurements with these tools. It includes instructions for organizing and conducting a field campaign. Throughout, there is a focus on the burgeoning field of imaging spectroscopy, which is revolutionizing our ability to characterize life remotely. Part 3 takes on an overarching issue for any effort to globalize biodiversity observations, the issue of scale. It addresses scale from two perspectives. The first is that of combining observations across varying spatial, temporal, and spectral resolutions for better understanding—that is, what scales and how. This is an area of ongoing research driven by a confluence of innovations in observation systems and rising computational capacity. The second is the organizational side of the scaling challenge. It explores existing frameworks for integrating multi-scale observations within global networks. The focus here is on what practical steps can be taken to organize multi-scale data and what is already happening in this regard. These frameworks include essential biodiversity variables and the Group on Earth Observations Biodiversity Observation Network (GEO BON). This book constitutes an end-to-end guide uniting the latest in research and techniques to cover the theory and practice of the remote sensing of plant biodiversity. In putting it together, the editors and their coauthors, all preeminent in their fields, have done a great service for those seeking to understand and conserve life on Earth—just when we need it most. For if the world is ever to construct a coordinated response to the planetwide crisis of biodiversity loss, it must first assemble adequate—and global—measures of what we are losing