Fractal analysis of leaf-texture properties as a tool for taxonomic and identification purposes: a case study with species from Neotropical Melastomataceae (Miconieae tribe)

Melastomataceae is a common and dominant family in Neotropical vegetation, with high species diversity which leads to a large variation in some morphological structures. Despite this, some species of Melastomataceae are very similar in their external leaf morphology, leading to difficulties in their identification without the presence of reproductive organs. Here we have proposed and tested a computer-aided texture-based approach used to correctly identify and distinguish leaves of some species of Melastomataceae that occur in a region of Neotropical savanna in Southeastern Brazil, also comparing it with other previously proposed approaches. The results demonstrated that our approach may clearly separate the studied species, analyzing the patterns of leaf texture (both adaxial and abaxial surfaces), and achieving better accuracy (100%) than other methods. Our work has suggested that leaf texture properties can be used as a new characteristic for identification, and as an additional source of information in taxonomic and systematic studies. As the method may be supervised by experts, it is also suitable for discrimination of species with high morphological plasticity, improving the automated discrimination task. This approach can be very useful for identification of species in the absence of reproductive material, and is a rapid and powerful tool for plant identification.CNPq (306628/2007-4; 484474/2007-3)FAPESP (08/57313-2

Leaf recognition for accurate plant classification.

Doctor of Philosophy in Computer Science, University of KwaZulu-Natal, Durban 2017.Plants are the most important living organisms on our planet because they are sources of energy and protect our planet against global warming. Botanists were the first scientist to design techniques for plant species recognition using leaves. Although many techniques for plant recognition using leaf images have been proposed in the literature, the precision and the quality of feature descriptors for shape, texture, and color remain the major challenges. This thesis investigates the precision of geometric shape features extraction and improved the determination of the Minimum Bounding Rectangle (MBR). The comparison of the proposed improved MBR determination method to Chaudhuri's method is performed using Mean Absolute Error (MAE) generated by each method on each edge point of the MBR. On the top left point of the determined MBR, Chaudhuri's method has the MAE value of 26.37 and the proposed method has the MAE value of 8.14. This thesis also investigates the use of the Convexity Measure of Polygons for the characterization of the degree of convexity of a given leaf shape. Promising results are obtained when using the Convexity Measure of Polygons combined with other geometric features to characterize leave images, and a classification rate of 92% was obtained with a Multilayer Perceptron Neural Network classifier. After observing the limitations of the Convexity Measure of Polygons, a new shape feature called Convexity Moments of Polygons is presented in this thesis. This new feature has the invariant properties of the Convexity Measure of Polygons, but is more precise because it uses more than one value to characterize the degree of convexity of a given shape. Promising results are obtained when using the Convexity Moments of Polygons combined with other geometric features to characterize the leaf images and a classification rate of 95% was obtained with the Multilayer Perceptron Neural Network classifier. Leaf boundaries carry valuable information that can be used to distinguish between plant species. In this thesis, a new boundary-based shape characterization method called Sinuosity Coefficients is proposed. This method has been used in many fields of science like Geography to describe rivers meandering. The Sinuosity Coefficients is scale and translation invariant. Promising results are obtained when using Sinuosity Coefficients combined with other geometric features to characterize the leaf images, a classification rate of 80% was obtained with the Multilayer Perceptron Neural Network classifier. Finally, this thesis implements a model for plant classification using leaf images, where an input leaf image is described using the Convexity Moments, the Sinuosity Coefficients and the geometric features to generate a feature vector for the recognition of plant species using a Radial Basis Neural Network. With the model designed and implemented the overall classification rate of 97% was obtained

Genotypic variation in climbing ability traits in a common bean RIL population

Climbing beans are vines that can be grown in either monoculture using wooden or bamboo trellises or in intercropping with other support crops such as maize, but in either case an important characteristic of climbing beans is their vegetative vigor and climbing ability. A range of climbing bean architecture exists; some are extremely vigorous producing more biomass at the top of the plant (type IVb), while others distribute biomass more uniformly across their the length of their vines (type IVa). Different types are selected by farmers in given situations, depending on climate, cropping system, harvesting method and growing period. Few studies have analyzed the inheritance of climbing ability in common bean or analyzed the interaction of this trait with soil fertility levels. Information about climbing ability and its component traits could be used by plant breeders to develop climbing bean ideotypes for different production systems. Therefore one of our research objectives has been to develop methods to analyze climbing bean growth and apply these to genetic mapping populations. In this research we analyzed a population of recombinant inbred lines derived from the cross of a climbing bean, G2333, by a bush bean, G19839, grown under high and low phosphorus treatments, for traits involved with climbing ability

Meiosis

Meiosis, the process of forming gametes in preparation for sexual reproduction, has long been a focus of intense study. Meiosis has been studied at the cytological, genetic, molecular and cellular levels. Studies in model systems have revealed common underlying mechanisms while in parallel, studies in diverse organisms have revealed the incredible variation in meiotic mechanisms. This book brings together many of the diverse strands of investigation into this fascinating and challenging field of biology

Functional analysis of candidate terpenoid biosynthetic genes isolated from grapevine

Thesis (PhDAgric)--Stellenbosch University, 2021.ENGLISH ABSTRACT: Terpenoids are a group of compounds found in various organisms, with diverse functions, and can be broadly grouped into primary or specialised (secondary) metabolites. This compound diversity is achieved from the universal precursors for terpenoids, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), through the activity of various enzymes. Isoprenyl diphosphate synthases (IDSs) incorporate the IPP and DMAPP precursors into compounds of varying lengths that can then serve as the substrate for terpene synthases (TPSs) to produce terpenes. Each of these steps incorporates the opportunity to further increase terpene diversity. In addition, terpenes can be modified into other products through the activity of various enzymes to increase the product range even further. Terpenoids play an important role in Vitis vinifera (grapevine), not only in the normal functioning of the plant, but also in more specialised roles involving plant–environment interactions. In terms of their economic value, terpenes, such as mono- and sesquiterpenes, contribute to wine aroma – which has supported the study of these compounds and how these metabolites are biosynthesised. Grapevine genome annotation has shown a moderately sized IDS gene family and a TPS gene family that has undergone extensive expansion. However, many of these genes have not been functionally characterised. Putative annotation based on sequences is not always accurate or does not provide a realistic indication of gene function. Functional characterisation of IDS and TPS genes involves heterologous expression followed by analysis of the produced compounds. In this study, various heterologous systems were used and evaluated with the aim of characterising grapevine genes that putatively encode IDS and TPS enzymes. In this study, the novel annotation of a eucalyptol synthase and the re-annotation of a previously characterised gene to α-thujene synthase was achieved. Various expression systems were assessed, with Saccharomyces cerevisiae deemed a viable alternative to the typical use of Escherichia coli. Different plant systems were also investigated, with Nicotiana benthamiana found to be a good option in terms of ease of use and results obtained. An in-depth study of geranylgeranyl diphosphate synthase (VviGGPS) was also conducted using an established transgenic tobacco population. The population was characterised in terms of morphology, physiology, and metabolites. The possible role of gibberellin was also determined based on the results of these analyses.AFRIKAANSE OPSOMMING: Terpene is ’n groep metaboliete wat in verskillende organismes voorkom, met ’n wye verskeidenheid van funksies, en wat breedvoerig in primêre of gespesialiseerde (sekondêre) metaboliete opgedeel kan word. Terpeen diversiteit word bewerkstellig vanaf die universele voorlopers, isopentenieldifosfaat (IPP) en dimetielallieldifosfaat (DMAPP), deur die aktiwiteit van verskeie ensieme. Isoprenieldifosfaat-sintases (IDSs) inkorporeer die IPP en DMAPP voorlopers binne-in verbindings van wisselende lengtes in wat dan as die substrate vir terpeen-sintases (TPSs) kan dien vir die biosintese van terpene. Elkeen van hierdie stappe bied ’n geleentheid om terpeen diversiteit te vermeerder. Terpene kan ook gemodifiseer word na ander produkte toe deur die aktiwiteit van verskeie ensieme om sodoende die terpeen produkreeks selfs meer te vermeerder. Terpene speel ’n belangrike rol in Vitis vinifera (wingerd); nie net in die normale funksionering van die plant nie, maar ook in ’n meer gespesialiseerde rol in plant–omgewing interaksies. In terme van ekonomiese waarde dra terpene soos mono- en seskwiterpene by tot die aroma van wyn – wat gedien het as ondersteuning vir die bestudering van hierdie verbindigs asook die biosintese daarvan. Annotering van die wingerd genoom het aangedui dat dit beskik oor ’n gemiddelde- grootte IDS geenfamilie en ’n TPS geenfamilie wat ekstensiewe vergroting ondergaan het. Baie van hierdie gene is egter nog nie gekarakteriseer in terme van funksie nie. Die vermeende benaming van gene gebaseer op nukleotied- of aminosuurvolgorde is ook nie altyd akkuraat nie of verskaf nie ’n realistiese indikasie van geenfunksie nie. Funksionele karakterisering van IDS en TPS gene behels heteroloë uitdrukking gevolg deur die analise van die geproduseerde metaboliete. Verskeie heteroloë sisteme is in hierdie studie gebruik en geëvalueer met die doel om wingerd gene wat kodeer vir vermeende IDS en TPS ensieme te karakteriseer. In hierdie studie is die nuwe annotering van ’n eukaliptol-sintase asook die annotasie van ’n voorheen gekaraktiseerde geen na α-thujene-sintase. Verskeie sisteme was ondersoek en Saccharomyces cerevisiae is gevind as ’n goeie alternatief tot die tipiese gebruik van Escherichia coli. Verskeie plantsisteme is ook oorweeg en Nicotiana benthamiana is gevind as ’n goeie opsie in terme van gebruikersvriendelikheid en resultate wat verkry is. ’n In-diepte studie van ’n geranielgeranieldifosfaat-sintase (VviGGPS) is ook uitgevoer deur die bestudering van ’n gevestigde transgeniese tabak populasie. Die populasie is gekaraktiriseer in terme van morfologie, fisiologie en metaboliete. Die moontlike rol van gibberelien gebasseer op hierdie analises, is ook bepaal.Doctora

Full Proceedings, 2018

Full conference proceedings for the 2018 International Building Physics Association Conference hosted at Syracuse University

Life Sciences Program Tasks and Bibliography for FY 1997

This document includes information on all peer reviewed projects funded by the Office of Life and Microgravity Sciences and Applications, Life Sciences Division during fiscal year 1997. This document will be published annually and made available to scientists in the space life sciences field both as a hard copy and as an interactive internet web page

Ways and Capacity in Archaeological Data Management in Serbia

Over the past year and due to the COVID-19 pandemic, the entire world has witnessed inequalities across borders and societies. They also include access to archaeological resources, both physical and digital. Both archaeological data creators and users spent a lot of time working from their homes, away from artefact collections and research data. However, this was the perfect moment to understand the importance of making data freely and openly available, both nationally and internationally. This is why the authors of this paper chose to make a selection of data bases from various institutions responsible for preservation and protection of cultural heritage, in order to understand their policies regarding accessibility and usage of the data they keep. This will be done by simple visits to various web-sites or data bases. They intend to check on the volume and content, but also importance of the offered archaeological heritage. In addition, the authors will estimate whether the heritage has adequately been classified and described and also check whether data is available in foreign languages. It needs to be seen whether it is possible to access digital objects (documents and the accompanying metadata), whether access is opened for all users or it requires a certain hierarchy access, what is the policy of usage, reusage and distribution etc. It remains to be seen whether there are public API or whether it is possible to collect data through API. In case that there is a public API, one needs to check whether datasets are interoperable or messy, requiring data cleaning. After having visited a certain number of web-sites, the authors expect to collect enough data to make a satisfactory conclusion about accessibility and usage of Serbian archaeological data web bases