Combining model structure identification and hybrid modelling for photo-production process predictive simulation and optimisation

Integrating physical knowledge and machine learning is a critical aspect of developing industrially focused digital twins for monitoring, optimisation, and design of microalgal and cyanobacterial photo-production processes. However, identifying the correct model structure to quantify the complex biological mechanism poses a severe challenge for the construction of kinetic models, while the lack of data due to the time-consuming experiments greatly impedes applications of most data-driven models. This study proposes the use of an innovative hybrid modelling approach that consists of a simple kinetic model to govern the overall process dynamic trajectory and a data-driven model to estimate mismatch between the kinetic equations and the real process. An advanced automatic model structure identification strategy is adopted to simultaneously identify the most physically probable kinetic model structure and minimum number of data-driven model parameters that can accurately represent multiple data sets over a broad spectrum of process operating conditions. Through this hybrid modelling and automatic structure identification framework, a highly accurate mathematical model was constructed to simulate and optimise an algal lutein production process. Performance of this hybrid model for long-term predictive modelling, optimisation, and online self-calibration is demonstrated and thoroughly discussed, indicating its significant potential for future industrial application.     

Morphological and molecular identification to secure cultivar maintenance and management of self-sterile Rubus arcticus

Background and Aims

Preservation of cultivar purity creates a particular challenge for plants that are self-incompatible, require insects for cross-pollination, and have easily germinating seeds and vigorously spreading rhizomes. As the fields must be planted with mixed populations, and a balance must be maintained between the cultivars to achieve effective pollination, methods for field monitoring of the relative density of different cultivars must be practical. Furthermore, a DNA-based method is needed for cultivar verification in the collections and outside of the growing season. The aim of this study was to develop both types of methods for Rubus arcticus (arctic bramble).

Methods

Morphological parameters were measured from six cultivars grown on three farms. Observations from the flowers and fruits included: petal and sepal number, flower diameter, arrangement of petals, size of calyx in relation to corolla, fruit weight, yield and soluble sugars. Observations from the leaves included: width and height of middle leaflet, shape of the base of terminal leaflet, shape of terminal leaflet, leaf margin serration and fingertip touch. The applicability of simple sequence repeat (SSR) or microsatellite DNA markers developed for red raspberry was tested on eight arctic bramble cultivars.

Key Results and Conclusions

Morphological and molecular identification methods were developed for R. arcticus. The best morphological characteristics were the length-to-width ratio of the middle leaflet and leaf margin serration. A particular characteristic, fingertip touch, was shown by electron microscopy to be related to the density and quality of the leaf hairs. Red raspberry SSR marker no. 126 proved to be applicable for differentiation of the eight arctic bramble cultivars tested. These identification methods are critical to secure the maintenance and management of R. arcticus. However, the challenges faced and approaches taken are equally applicable to other species with similar biology.     

Chemical analysis of mucus from certain land snails under Egyptian conditions

Abstract

The present investigation was carried out to study the chemical analysis of the mucus of three common land snails, Eobania vermiculata, Theba pisana and Monacha obstructa, and identification of the chemical compositions by using GC-MS. Results revealed that several variations in composition were observed between all species. Oxime, methoxy-phenyl and cyclotrisiloxane, hexamethyl were major components found that in three species, the total areas detected were 86.23, 76.83 and 70.83, respectively. This different composition of mucus may be due to differences from one species to another; different mechanical properties (function) are influenced by external factors such as temperature, humidity, light intensity, soil conditions and food supply.     

Characterisation of Pectobacterium carotovorum causing soft rot on Kalanchoe gastonis-bonnierii in Malaysia

Soft rot disease can be found worldwide on fleshy storage tissues of fruits, vegetables and ornamentals. The soft rot Pectobacterium carotovorum subsp. carotovorum (Pcc) is an important pathogen of Kalanchoe spp. and other ornamental plants. The disease occurs on crops in the field, greenhouses and during transit, resulting great economic damages. The economic importance of crop loss by soft rot bacteria varies by severity of the disease and value of the crop. A destructive disease on Kalanchoe gastonis-bonnierii was observed in commercial ornamental plant greenhouses in Cameron highland and Melaka, Malaysia in 2011. Samples suspected to be infested with Pectobacterium spp. were brought to the laboratory. In pathogenicity test, a suspension of 10^6?CFU/ml of strains was able to cause soft rot on leaves and stems. A 434?bp banding pattern on 1% agarose gel was produced in polymerase chain reaction (PCR) amplification of pectate lyase encoding gene (Pel gene). PCR amplification of the intergenic transcribed spacer (ITS) (16S–23S rRNA) ITS region with G₁ and L₁ primers produced two main bands at about 540 and 570?bp. The ITS-PCR products were digested with RsaI restriction enzyme. For discrimination of the P. carotovorum subsp. carotovorum (Pcc) from P. carotovorum subsp. odoriferum (Pco), all isolates subjected to α-methyl glucoside test. All isolates were identified as Pcc based on phenotypic and molecular methods. This is the first report of soft rot disease caused by P. carotovorum subsp. carotovorum on K. gastonis-bonnierii, in Malaysia.     

Comparing methods for metabolic network analysis and an application to metabolic engineering

Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.     

Characterization of seven novel mutations on the HEXB gene in French Sandhoff patients

Sandhoff disease (SD) is an autosomal recessive lysosomal storage disease caused by mutations in the HEXB gene encoding the beta subunit of hexosaminidases A and B, two enzymes involved in GM2 ganglioside degradation. Eleven French Sandhoff patients with infantile or juvenile forms of the disease were completely characterized using sequencing of the HEXB gene. A specific procedure was developed to facilitate the detection of the common 5′-end 16 kb deletion which was frequent (36% of the alleles) in our study. Eleven other disease-causing mutations were found, among which four have previously been reported (c.850C>T, c.793T>G, c.115del and c.800_817del). Seven mutations were completely novel and were analyzed using molecular modelling. Two deletions (c.176del and c.1058_1060del), a duplication (c.1485_1487dup) and a nonsense mutation (c.552T>G) were predicted to strongly alter the enzyme spatial organization. The splice mutation c.558+5G>A affecting the intron 4 consensus splice site led to a skipping of exon 4 and to a truncated protein (p.191X). Two missense mutations were found among the patients studied. The c.448A>C mutation was probably a severe mutation as it was present in association with the known c.793T>G in an infantile form of Sandhoff disease and as it significantly modified the N-terminal domain structure of the protein. The c.171G>C mutation resulting in a p.W57C amino acid substitution in the N-terminal region is probably less drastic than the other abnormalities as it was present in a juvenile patient in association with the c.176del. Finally, this study reports a rapid detection of the Sandhoff disease-causing alleles facilitating genetic counselling and prenatal diagnosis in at-risk families.     

馆藏植物标本与iFlora

构建准确、有效的物种遗传信息库并运用其作为主要的物种鉴定检索数据库,是新一代植物志（iFlora）与传统植物志的本质区别。采集并准确鉴定数以万计的植物样品用于建立遗传信息库存在一定困难,随着遗传信息获取技术的快速发展,使馆藏植物标本成为获取遗传信息的重要补充,并具有提升遗传信息库建设速度和可靠性的较大潜能。本文结合已有的研究和实验室多年工作实践,论述了植物标本作为iFlora物种遗传信息提取材料的可行性和不可替代性;总结了标本遗传信息提取过程中的主要困难和存在问题,并提出一些解决方法;阐述了使用馆藏标本特别是利用模式标本材料构建遗传信息标准库对iFlora构建的重要作用和意义。     

New species and records of Stigmaeidae (Acari: Prostigmata) from New Zealand - ID. Genus Stigmaeus Koch

Abstract

Stigmaeus arboricola, S. montanus, S. luxtoni, and S. novazealandicus are described as new species, and the larva of S. loadmani is described. Several new records are noted, and a key is given to the New Zealand species of Stigmaeus.     

Likely future extirpation of another Asian river dolphin: The critically endangered population of the Irrawaddy dolphin in the Mekong River is small and declining

The population of Irrawaddy dolphins that occupies the Mekong River in southern Lao People's Democratic Republic and Cambodia is classified as Critically Endangered by the IUCN. Based on capture‐recapture of photo‐identified individuals, we estimated that the total population numbered 93 ±  SE 3.90 individuals (95% CI 86–101), as of April 2007. The combined photo‐identification and carcass recovery program undertaken from 2001 to 2007 established that the Irrawaddy dolphin population inhabiting the Mekong River has reached a critical point with regards to its continued survival, where immediate research and management actions are required to greatly reduce adult mortality, and establish the cause of newborn mortality. In addition, community consultation is required to initiate, and evaluate, urgently required conservation measures. An ongoing well‐designed combined program of abundance estimation (i.e., photo‐identification) and carcass recovery is required to monitor total population size and mortality rates, to inform and evaluate management initiatives. The conclusions of this paper are likely generic to river dolphin populations, particularly where photo‐identification is possible.