Monitoring Cascading Changes of Resources in the Kubernetes Control Plane

Kubernetes is a container management system that has many automated functionalities. Those functionalities are managed by configuring objects and resources in the control plane. Since most objects change their state depending on other objects' states, a change propagates to other objects in a chain. As cluster availability is influenced by the time required for these cascading changes, it is essential to make the propagations measurable and shed light on the behavior of the Kubernetes control plane. However, it is not easy because each object constantly monitors other objects' status and acts autonomously in response to their changes to play its role. In this paper, we propose a measurement system that outputs objects' change logs published from the API server in the control plane and assists in analyzing the time of cascading changes between objects by utilizing the relationships among resources. With a practical change scenario, our system is confirmed that it can measure change propagation times within a cascading change. Also, measurements on the system itself showed it has a small CPU and memory footprint

Towards the Design of a Synchronous Virtual Learning System

The field of education has undoubtedly been affected by the penetrating influence of information and communication technology, characterized by improved access to the internet, and the increasing use of computing devices. However, education in Africa generally and specifically in Nigeria and other developing countries still face a 21st Century challenge in making education available and accessible to all. To this end therefore, this paper presents a conceptual approach, as to how tailor made e-learning services could be realized and integrated with a real time video conference server and any existing learning management system in order to facilitate a synchronous virtual learning environment in making education accessible and available to both remote students (distance learning students) and onsite users in Universities and other related educational institutes. It proposes a functional framework to exemplify educational services such as file sharing to enhance collaboration, a digital resource center for retrieval of both free and paid relevant academic resource. A conference room for real time classroom participation which learning platform should provide in order to enhance both teaching and learning performance of course instructors and their students respectively is also proposed. It provides an operational design which describes how custom made e-learning portal integrated with an Open source Video Conference server could be realized, in facilitating a synchronous virtual learning service. Furthermore, it proposes a Virtual Learning Network architecture to show how both remote and onsite students could optimize quality network access in realizing these electronic learning services

Physico-chemical and microbiological changes in commercial tilapia (Oreochromis niloticus) during cold storage

[EN] The microbiological and chemical processes are the main responsible for deterioration of fresh fish. Therefore, it is essential to avoid these processes by applying good manufacturing practices during fish handling, distribution and storage. Objective: The aim of this paper was to evaluate the physico-chemical and microbial changes in commercial tilapia (Oreochromis niloticus) during cold storage in order to establish the shelf life since its arrival at the supermarket. Methods: 27 aquacultured tilapia specimens were analyzed at 0, 2, 4, and 7 days of storage at 4ºC. Measurements of texture, color, water holding capacity, total volatile basic nitrogen (TVB-N), thiobarbituric acid index, ATP-related compounds, as well as microbial analyses were carried out. Results: The TVB-N content was high at the beginning of the study, remaining stable during the storage. Lipid oxidation of samples was minimum, so this process did not contribute to the fish spoilage. It was observed the breakdown of inosine-5’- monophosphate (IMP) into Ino (inosine), and Ino into Hx (hypoxantine). The texture parameters and colour underwent changes as a consequence of the fish spoilage. Low microbial counts were observed at day 0, but Enterobacteriaceae and mesophilic counts gradually increased throughout storage. Conclusions: The K1-value showed the progressive spoilage of the fish during the cold storage. The decrease of hardness and firmness confirmed the loss of quality throughout the time of study. The low microbial counts at the beginning of the study demonstrated the good quality of the tilapia; however, the increase of the mesophilic counts at the end of the studied period showed that tilapia was not fit for human consumption at day 7.[ES] Antecedentes: Los procesos microbiológicos y químicos son los principales responsables del deterioro del pescado fresco. Por tanto, es esencial evitar estos procesos aplicando buenas prácticas de fabricación durante la manipulación, distribución y almacenamiento del pescado. Objetivo: El objetivo de este trabajo fue evaluar los cambios físico-químicos y microbiológicos en tilapia comercial (Oreochromis niloticus) durante el almacenamiento refrigerado con el fin de establecer la vida útil desde su llegada al supermercado. Métodos: 27 especímenes de tilapia fueron analizados a día 0, 2, 4 y 7 de almacenamiento a 4 ºC. Se llevaron a cabo medidas de textura, color, capacidad de retención de agua, nitrógeno básico volátil total (N-BVT), índice del ácido tiobarbitúrico, compuestos relacionados con el ATP, así como análisis microbianos. Resultados: El contenido en N-BVT fue alto al principio del estudio, siendo estable durante el almacenamiento. La oxidación lipídica de las muestras fue mínima, por lo que este proceso no contribuyó al deterioro del pescado. Se observó la degradación de inosina-5’- monofosfato (IMP) a Ino (inosina), y de Ino a Hx (hipoxantina). Los parámetros de textura y color sufrieron cambios como consecuencia del deterioro del pescado. Se observaron bajos recuentos microbianos a día 0, pero los recuentos de Enterobacteriaceae y de mesófilos aumentaron gradualmente durante el almacenamiento. Conclusiones: El valor K1 mostró el deterioro progresivo del pescado durante el almacenamiento en refrigeración. La disminución de dureza y firmeza confirmó la pérdida de calidad a lo largo del tiempo de estudio. Los bajos recuentos microbianos al principio del estudio demostraron la buena calidad de la tilapia; sin embargo, el aumento de los recuentos de mesófilos al final del periodo estudiado mostraron que la tilapia no era adecuada para el consumo humado a día 7.Gutiérrez Guzmán, N.; Fernández Segovia, I.; Fuentes López, A.; Ruiz Rico, M.; Barat Baviera, JM. (2015). Physico-chemical and microbiological changes in commercial tilapia (Oreochromis niloticus) during cold storage. Revista Vitae. 22(2):140-147. doi:10.17533/udea.vitae.v22n2a08S14014722

Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation

Background: Cyanobacteria are potential sources of renewable chemicals and biofuels and serve as model organisms for bacterial photosynthesis, nitrogen fixation, and responses to environmental changes. Anabaena (Nostoc) sp. strain PCC 7120 (hereafter Anabaena) is a multicellular filamentous cyanobacterium that can "fix" atmospheric nitrogen into ammonia when grown in the absence of a source of combined nitrogen. Because the nitrogenase enzyme is oxygen sensitive, Anabaena forms specialized cells called heterocysts that create a microoxic environment for nitrogen fixation. We have employed directional RNA-seq to map the Anabaena transcriptome during vegetative cell growth and in response to combined-nitrogen deprivation, which induces filaments to undergo heterocyst development. Our data provide an unprecedented view of transcriptional changes in Anabaena filaments during the induction of heterocyst development and transition to diazotrophic growth. Results: Using the Illumina short read platform and a directional RNA-seq protocol, we obtained deep sequencing data for RNA extracted from filaments at 0, 6, 12, and 21 hours after the removal of combined nitrogen. The RNA-seq data provided information on transcript abundance and boundaries for the entire transcriptome. From these data, we detected novel antisense transcripts within the UTRs (untranslated regions) and coding regions of key genes involved in heterocyst development, suggesting that antisense RNAs may be important regulators of the nitrogen response. In addition, many 5' UTRs were longer than anticipated, sometimes extending into upstream open reading frames (ORFs), and operons often showed complex structure and regulation. Finally, many genes that had not been previously identified as being involved in heterocyst development showed regulation, providing new candidates for future studies in this model organism. Conclusions: Directional RNA-seq data were obtained that provide comprehensive mapping of transcript boundaries and abundance for all transcribed RNAs in Anabaena filaments during the response to nitrogen deprivation. We have identified genes and noncoding RNAs that are transcriptionally regulated during heterocyst development. These data provide detailed information on the Anabaena transcriptome as filaments undergo heterocyst development and begin nitrogen fixation

Elucidating Genome Structure Evolution by Analysis of Isoapostatic Gene Clusters using Statistics of Variance of Gene Distances

Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In related genomes, clusters of homologous gene pairs serve as evidence for candidate homologous regions, which make up genomic core. Previous studies on the structural organization of bacterial genomes revealed that basic backbone of genomic core is interrupted by genomic islands. Here, we applied statistics using variance of distances as a measure to classify conserved genes within a set of genomes according to their “isoapostatic” relationship, which keeps nearly identical distances of genes. The results of variance statistics analysis of cyanobacterial genomes including Prochlorococcus, Synechococcus, and Anabaena indicated that the conserved genes are classified into several groups called “virtual linkage groups (VLGs)” according to their positional conservation of orthologs over the genomes analyzed. The VLGs were used to define mosaic domain structure of the genomic core. The current model of mosaic genomic domains can explain global evolution of the genomic core of cyanobacteria. It also visualizes islands of lateral gene transfer. The stability and the robustness of the variance statistics are discussed. This method will also be useful in deciphering the structural organization of genomes in other groups of bacteria

Group 3 sigma factor gene, sigJ, a key regulator of desiccation tolerance, regulates the synthesis of extracellular polysaccharide in cyanobacterium Anabaena sp. strain PCC 7120

The changes in the expression of sigma factor genes during dehydration in terrestrial Nostoc HK-01 and aquatic Anabaena PCC 7120 were determined. The expression of the sigJ gene in terrestrial Nostoc HK-01, which is homologous to sigJ (alr0277) in aquatic Anabaena PCC 7120, was significantly induced in the mid-stage of dehydration. We constructed a higher-expressing transformant of the sigJ gene (HE0277) in Anabaena PCC 7120, and the transformant acquired desiccation tolerance. The results of Anabaena oligonucleotide microarray experiments showed that a comparatively large number of genes relating to polysaccharide biosynthesis were upregulated in the HE0277 cells. The extracellular polysaccharide released into the culture medium of the HE0277 cells was as much as 3.2-fold more than that released by the control cells. This strongly suggests that the group 3 sigma factor gene sigJ is fundamental and conducive to desiccation tolerance in these cyanobacteria

Cyanobacterial Cell Lineage Analysis of the Spatiotemporal hetR Expression Profile during Heterocyst Pattern Formation in Anabaena sp. PCC 7120

Diazotrophic heterocyst formation in the filamentous cyanobacterium, Anabaena sp. PCC 7120, is one of the simplest pattern formations known to occur in cell differentiation. Most previous studies on heterocyst patterning were based on statistical analysis using cells collected or observed at different times from a liquid culture, which would mask stochastic fluctuations affecting the process of pattern formation dynamics in a single bacterial filament. In order to analyze the spatiotemporal dynamics of heterocyst formation at the single filament level, here we developed a culture system to monitor simultaneously bacterial development, gene expression, and phycobilisome fluorescence. We also developed micro-liquid chamber arrays to analyze multiple Anabaena filaments at the same time. Cell lineage analyses demonstrated that the initial distributions of hetR::gfp and phycobilisome fluorescence signals at nitrogen step-down were not correlated with the resulting distribution of developed heterocysts. Time-lapse observations also revealed a dynamic hetR expression profile at the single-filament level, including transient upregulation accompanying cell division, which did not always lead to heterocyst development. In addition, some cells differentiated into heterocysts without cell division after nitrogen step-down, suggesting that cell division in the mother cells is not an essential requirement for heterocyst differentiation

The Smallest Known Genomes of Multicellular and Toxic Cyanobacteria: Comparison, Minimal Gene Sets for Linked Traits and the Evolutionary Implications

Cyanobacterial morphology is diverse, ranging from unicellular spheres or rods to multicellular structures such as colonies and filaments. Multicellular species represent an evolutionary strategy to differentiate and compartmentalize certain metabolic functions for reproduction and nitrogen (N2) fixation into specialized cell types (e.g. akinetes, heterocysts and diazocytes). Only a few filamentous, differentiated cyanobacterial species, with genome sizes over 5 Mb, have been sequenced. We sequenced the genomes of two strains of closely related filamentous cyanobacterial species to yield further insights into the molecular basis of the traits of N2 fixation, filament formation and cell differentiation. Cylindrospermopsis raciborskii CS-505 is a cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis brookii D9 from Brazil synthesizes neurotoxins associated with paralytic shellfish poisoning (PSP). Despite their different morphology, toxin composition and disjunct geographical distribution, these strains form a monophyletic group. With genome sizes of approximately 3.9 (CS-505) and 3.2 (D9) Mb, these are the smallest genomes described for free-living filamentous cyanobacteria. We observed remarkable gene order conservation (synteny) between these genomes despite the difference in repetitive element content, which accounts for most of the genome size difference between them. We show here that the strains share a specific set of 2539 genes with >90% average nucleotide identity. The fact that the CS-505 and D9 genomes are small and streamlined compared to those of other filamentous cyanobacterial species and the lack of the ability for heterocyst formation in strain D9 allowed us to define a core set of genes responsible for each trait in filamentous species. We presume that in strain D9 the ability to form proper heterocysts was secondarily lost together with N2 fixation capacity. Further comparisons to all available cyanobacterial genomes covering almost the entire evolutionary branch revealed a common minimal gene set for each of these cyanobacterial traits

Genomic Structure of an Economically Important Cyanobacterium, Arthrospira (Spirulina) platensis NIES-39

A filamentous non-N2-fixing cyanobacterium, Arthrospira (Spirulina) platensis, is an important organism for industrial applications and as a food supply. Almost the complete genome of A. platensis NIES-39 was determined in this study. The genome structure of A. platensis is estimated to be a single, circular chromosome of 6.8 Mb, based on optical mapping. Annotation of this 6.7 Mb sequence yielded 6630 protein-coding genes as well as two sets of rRNA genes and 40 tRNA genes. Of the protein-coding genes, 78% are similar to those of other organisms; the remaining 22% are currently unknown. A total 612 kb of the genome comprise group II introns, insertion sequences and some repetitive elements. Group I introns are located in a protein-coding region. Abundant restriction-modification systems were determined. Unique features in the gene composition were noted, particularly in a large number of genes for adenylate cyclase and haemolysin-like Ca2+-binding proteins and in chemotaxis proteins. Filament-specific genes were highlighted by comparative genomic analysis

Discrepancy between magnetic resonance imaging and cranial nerve neuropathies associated with the involvement of diffuse large B-cell lymphoma（DLBL）.

An 83-year-old female developed diffuse large B-cell lymphoma（DLBL） of the left nasal cavity. Complete remission was achieved after two courses of Rituximab and CHOP（R-CHOP） . During the fourth course of R-CHOP, sensory disturbance and palsy of the left face developed. Left trigeminal nerve swelling was observed in magnetic resonance imaging（MRI） followed by double vision in the left eye, and MRI revealed swelling of both trigeminal nerves but not of the abducens nerve. Although the swelling of the trigeminal nerves and the double vision subside after administration of prednisolone, the palsy of the left face persisted. Two months after the fourth course of R-CHOP, symptoms of the palsy of the left face progressed and palsy of the right face, double vision, and palsy of the left facialis nerve developed. Then,blepharoptosis of the right eye developed and palsy of the right oculomotorius nerve was observed. MRI showed the presence of trigeminal nerve and oculomotorius nerve swelling but no swelling of the other cranial nerves. Furthermore, skin eruption developed around the left eye.Cytology of this lesion revealed the invasion of lymphoma cells