This document summarizes the characteristics of eubacteria. Eubacteria are single-celled prokaryotic microorganisms that are enclosed by a cell wall made of peptidoglycans. They lack membrane-bound organelles and reproduce through binary fission. The document further describes the key characteristics of five major phyla of eubacteria: Chlamydias, Cyanobacteria, Gram-positive bacteria, Proteobacteria, and Spirochetes. Examples of common eubacteria, such as Escherichia coli and Streptococcus pneumoniae, are also provided.
1. The first person to observe living microorganisms using a microscope he invented was Antony van Leeuwenhoek in 1674, when he saw bacteria in dental plaque.
2. Bacteria are the most common and diverse type of prokaryotes, ranging in size from 0.2 to 2.0 μm and having a variety of shapes.
3. Bacterial cell walls are composed of peptidoglycan, while archaea cell walls contain other components like glycoproteins or polysaccharides.
Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles.
2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species.
3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria).
This document provides an overview of the classification of microorganisms. It discusses how organisms are grouped into three domains - archaea, bacteria, and eukarya - based on cell structure. Within these domains, microorganisms can be further classified based on various characteristics like cell structure, metabolism, temperature and pH optima, oxygen requirements, morphology, gram staining, presence of flagella, and ability to form spores. Bacteria, fungi, and archaea are described in more detail with examples provided for different groups.
The document discusses the five kingdom classification system proposed by Whittaker in 1969. The five kingdoms are Monera (prokaryotes), Protista (unicellular eukaryotes), Fungi (includes molds and mushrooms), Plantae (multicellular plants), and Animalia (includes animals). Each kingdom is defined based on characteristics such as cell structure, nutrition, and lifestyle. Monera includes bacteria and blue-green algae. Protista includes organisms like amoebas and euglenas. Fungi are saprophytic and include yeasts and molds. Plantae are autotrophic and multicellular. Animalia are heterotrophic and include insects,
This document discusses the major systems of biological classification that have been proposed over time. It begins by outlining Linnaeus' original two kingdom system (plants and animals), followed by Haeckel's three kingdom system (adding protists), Copeland's four kingdom system (splitting protists and adding monera), and Whittaker's influential five kingdom system (monera, protista, fungi, plants, animals). It then provides characteristics of each kingdom in Whittaker's five kingdom system and compares their key attributes.
This document summarizes the characteristics of eubacteria. Eubacteria are single-celled prokaryotic microorganisms that are enclosed by a cell wall made of peptidoglycans. They lack membrane-bound organelles and reproduce through binary fission. The document further describes the key characteristics of five major phyla of eubacteria: Chlamydias, Cyanobacteria, Gram-positive bacteria, Proteobacteria, and Spirochetes. Examples of common eubacteria, such as Escherichia coli and Streptococcus pneumoniae, are also provided.
1. The first person to observe living microorganisms using a microscope he invented was Antony van Leeuwenhoek in 1674, when he saw bacteria in dental plaque.
2. Bacteria are the most common and diverse type of prokaryotes, ranging in size from 0.2 to 2.0 μm and having a variety of shapes.
3. Bacterial cell walls are composed of peptidoglycan, while archaea cell walls contain other components like glycoproteins or polysaccharides.
Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles.
2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species.
3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria).
This document provides an overview of the classification of microorganisms. It discusses how organisms are grouped into three domains - archaea, bacteria, and eukarya - based on cell structure. Within these domains, microorganisms can be further classified based on various characteristics like cell structure, metabolism, temperature and pH optima, oxygen requirements, morphology, gram staining, presence of flagella, and ability to form spores. Bacteria, fungi, and archaea are described in more detail with examples provided for different groups.
The document discusses the five kingdom classification system proposed by Whittaker in 1969. The five kingdoms are Monera (prokaryotes), Protista (unicellular eukaryotes), Fungi (includes molds and mushrooms), Plantae (multicellular plants), and Animalia (includes animals). Each kingdom is defined based on characteristics such as cell structure, nutrition, and lifestyle. Monera includes bacteria and blue-green algae. Protista includes organisms like amoebas and euglenas. Fungi are saprophytic and include yeasts and molds. Plantae are autotrophic and multicellular. Animalia are heterotrophic and include insects,
This document discusses the major systems of biological classification that have been proposed over time. It begins by outlining Linnaeus' original two kingdom system (plants and animals), followed by Haeckel's three kingdom system (adding protists), Copeland's four kingdom system (splitting protists and adding monera), and Whittaker's influential five kingdom system (monera, protista, fungi, plants, animals). It then provides characteristics of each kingdom in Whittaker's five kingdom system and compares their key attributes.
This document summarizes the key points of the five kingdom classification system proposed by R.H. Whittaker which includes Monera, Protista, Fungi, Plantae and Animalia. It provides details on the characteristics of each kingdom, including examples of organisms that fall under each kingdom. The kingdoms are differentiated based on factors like cell structure, nutrition, reproduction and phylogenetic relationships. Viruses and lichens are also briefly discussed.
Bacteria are single-celled microorganisms that come in a variety of shapes and live in many environments. They were first observed by Van Leeuwenhoek in 1676 and named by Ehrenberg in 1828. Bacteria are prokaryotic, lacking organelles like nuclei, and reproduce through binary fission. There are four main types - rod-shaped bacilli like E. coli, spherical cocci like streptococci, spiral-shaped spirilla, and comma-shaped vibrios like V. cholerae. Bacteria can be helpful by increasing soil fertility, aiding digestion, and creating antibiotics, but can also be harmful as pathogens causing diseases or by contaminating food.
This document discusses the classification of microorganisms. It describes the differences between bacteria, archaea, and eukarya. It discusses the binominal nomenclature system developed by Carolus Linnaeus to classify organisms. It also describes Woese's three domain system that divides organisms into the domains of Archaea, Bacteria, and Eukarya. Finally, it provides details on the classification and characteristics of fungi, algae, protozoa, viruses, and bacteria.
This document discusses different branches of microbiology including bacteriology, virology, phycology, and mycology. It provides information on each branch such as:
Bacteriology studies bacteria morphology, ecology, and biochemistry. Virology is the study of viruses and their classification into groups based on shape. Phycology is the study of algae, which are important primary producers. Mycology is the study of fungi and their characteristics such as being eukaryotic and reproducing through spores.
General features of Proteobacteria, alpha Proteobacteria
subscribe youtube channel: Dharmesh Sherathia
https://www.youtube.com/watch?v=JxOIqxYmerk&t=348s
join me on insta @dharmesh.biology
Classification of Microorganisms 2019.pptxssuser504dda
1. Microorganisms are classified through taxonomy, which involves identification, classification, and nomenclature of organisms.
2. Taxonomic classification categories arrange species in a hierarchical order from domain to genus. Identification techniques include microscopy, culture characteristics, biochemical tests, and nucleic acid analysis.
3. Bacteria can be classified by morphology, staining, culture characteristics, oxygen requirements, metabolism, and environmental tolerances. Cocci, bacilli, vibrios, spirochetes, and spirilla are morphological groups.
This document provides information on bacteria morphology and identification. It discusses that bacteria are microscopic, unicellular organisms that can perform essential life functions. It describes different bacterial shapes including cocci, bacilli, vibrios, spirilla, and spirochaetes. Gram staining is used to classify bacteria as either gram positive or gram negative. Common gram positive cocci like staphylococci and streptococci are examined in detail. Requirements for bacterial growth such as nutrients, oxygen, temperature, and pH are also reviewed.
This document discusses the classification of microorganisms. It describes the three domain system proposed by Carl Woese which divides organisms into Archaea, Bacteria and Eukarya. It then provides details on the characteristics of fungi, algae, protozoa, viruses and bacteria; and discusses methods used to identify bacteria including biochemical tests and serological tests.
This document summarizes R.H. Whittaker's five kingdom classification system, which includes the kingdoms of Monera, Protista, Fungi, Plantae, and Animalia.
[1] Kingdom Monera includes bacteria, which are unicellular prokaryotes found everywhere that lack nuclei and organelles. They can be autotrophic through photosynthesis or chemosynthesis, or heterotrophic through parasitism or saprophytism.
[2] Kingdom Protista contains unicellular eukaryotic organisms that are autotrophic or heterotrophic, including diatoms, algae, dinoflagellates, and protozoa.
[3
Bacteria are microbes with a cell structure simpler than that of many other organisms. Their control centre, containing the genetic information, is contained in a single loop of DNA. Some bacteria have an extra circle of genetic material called a plasmid rather than a nucleus. The plasmid often contains genes that give the bacterium some advantage over other bacteria. For example it may contain a gene that makes the bacterium resistant to a certain antibiotic.
Bacteria are classified into five groups according to their basic shapes: spherical (cocci), rod (bacilli), spiral (spirilla), comma (vibrios) or corkscrew (spirochaetes). They can exist as single cells, in pairs, chains or clusters.
Bacteria are unicellular prokaryotic organisms that are found everywhere and are very abundant. They can thrive in extreme conditions where other organisms cannot live. Bacterial cells are typically much smaller than human cells. Bacteria come in a variety of shapes including spherical (cocci), rod-shaped (bacilli), spiral, and comma-shaped. The shape of a bacterial cell is an important characteristic that is specific to its species and can affect its pathogenicity, motility, and other traits. Common bacterial shapes include cocci arranged in pairs, chains, and clusters, as well as rod-shaped bacilli arranged singly or attached in pairs or chains.
The documents discuss the Kingdom Eubacteria, which contains unicellular prokaryotes that reproduce by binary fission. Eubacteria are classified by their gram staining and include four major phyla: Cyanobacteria, which are photosynthetic; Spirochetes, which have a spiral shape and can cause diseases; and Gram-positive bacteria, which differ from Gram-negative bacteria in their cell wall composition and antibiotic susceptibility. The documents explore the structural features and functions of Eubacteria as well as methods for identifying and classifying them.
A. Protists are a diverse group of unicellular or multicellular eukaryotic organisms that include important pathogens. B. Helminth parasites like roundworms and flatworms are often identified microscopically and can infect the intestines or other tissues. C. Fungi are eukaryotic organisms with chitin cell walls that can be unicellular or multicellular, including medically important molds, yeasts, and dermatophytes. D. Algae include unicellular and multicellular photosynthetic protists used to produce industrial compounds like agar. E. Lichens are a symbiotic partnership between fungi and algae or cyanobacteria that
MICROBIOLOGY QUICK LEARNFood MicrobiologyBACTERIA- Cultural Characteristics...Saajida Sultaana
Bacteria are important in food microbiology. They can cause food spoilage and illness, but some species are beneficial. Bacteria have specific nutrient and environmental needs. Their cultural characteristics include morphology, encapsulation, endospores, and cell aggregates. Morphological observation identifies size, shape, and structures. Encapsulation and endospores help bacteria survive harsh conditions. Some bacteria form chains or clumps. Their growth produces chemical changes and discolors or textures food. Understanding bacterial growth factors is key to food preservation and preventing spoilage.
Bacteria are classified in several ways:
1. By staining (Gram positive/negative, acid-fast), shape (cocci, bacilli), motility, environment (aerobic/anaerobic).
2. The bacterial cell has a cell wall, cell membrane, flagella/fimbriae and cytoplasm. The cell wall provides structure and protection through its peptidoglycan layer.
3. Bacteria are further classified based on nutrition sources, temperature, pH and salt tolerance ranges they thrive in. Most bacteria serve important ecological roles while some can cause disease.
This document provides information about biology and the classification of living organisms. It discusses the following key points:
- Biology is the science of living organisms and life processes. Modern biology integrates with other fields like chemistry and physics.
- Characteristics of living things include growth, reproduction, metabolism, response to stimuli, homeostasis, and evolution.
- Organisms are classified and grouped into a hierarchy of taxa including species, genus, family, order, class, phylum, and kingdom.
- The five kingdom system classifies organisms into Monera, Protista, Fungi, Plantae, and Animalia based on characteristics like cell structure, nutrition, and lifestyle. Examples of groups within each
This document provides an introduction and overview of gram-negative bacteria. It discusses their key characteristics and classification. Specifically, it summarizes several genera of gram-negative bacteria, including Pseudomonas, Xanthomonas, Azotobacter, Rhizobium, Methylococcus, Acetobacter, and Legionella. It also describes the families they belong to, such as Pseudomonadaceae, Azotobacteraceae, and Legionellaceae.
- Microorganisms play key roles in human health, agriculture, food production, and the environment. They can cause infectious diseases but have also helped control diseases through vaccines and antibiotics. Microbes aid agriculture through nitrogen fixation and by enabling ruminant digestion. They are crucial to food industries like dairying and brewing through fermentation. Some microbes also produce biofuels like methane and ethanol. Overall, microorganisms both threaten and greatly benefit human lives and activities.
Prokaryotes include bacteria and archaea. Bacteria were first observed in 1674 and include diverse species found in many habitats. Prokaryotes are single-celled without internal membranes and reproduce through binary fission. Major groups include eubacteria like E. coli and archaea found in extreme environments like hot springs or salt lakes. Bacteria play important roles in ecosystems through processes like nitrogen fixation and photosynthesis.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
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This document summarizes the key points of the five kingdom classification system proposed by R.H. Whittaker which includes Monera, Protista, Fungi, Plantae and Animalia. It provides details on the characteristics of each kingdom, including examples of organisms that fall under each kingdom. The kingdoms are differentiated based on factors like cell structure, nutrition, reproduction and phylogenetic relationships. Viruses and lichens are also briefly discussed.
Bacteria are single-celled microorganisms that come in a variety of shapes and live in many environments. They were first observed by Van Leeuwenhoek in 1676 and named by Ehrenberg in 1828. Bacteria are prokaryotic, lacking organelles like nuclei, and reproduce through binary fission. There are four main types - rod-shaped bacilli like E. coli, spherical cocci like streptococci, spiral-shaped spirilla, and comma-shaped vibrios like V. cholerae. Bacteria can be helpful by increasing soil fertility, aiding digestion, and creating antibiotics, but can also be harmful as pathogens causing diseases or by contaminating food.
This document discusses the classification of microorganisms. It describes the differences between bacteria, archaea, and eukarya. It discusses the binominal nomenclature system developed by Carolus Linnaeus to classify organisms. It also describes Woese's three domain system that divides organisms into the domains of Archaea, Bacteria, and Eukarya. Finally, it provides details on the classification and characteristics of fungi, algae, protozoa, viruses, and bacteria.
This document discusses different branches of microbiology including bacteriology, virology, phycology, and mycology. It provides information on each branch such as:
Bacteriology studies bacteria morphology, ecology, and biochemistry. Virology is the study of viruses and their classification into groups based on shape. Phycology is the study of algae, which are important primary producers. Mycology is the study of fungi and their characteristics such as being eukaryotic and reproducing through spores.
General features of Proteobacteria, alpha Proteobacteria
subscribe youtube channel: Dharmesh Sherathia
https://www.youtube.com/watch?v=JxOIqxYmerk&t=348s
join me on insta @dharmesh.biology
Classification of Microorganisms 2019.pptxssuser504dda
1. Microorganisms are classified through taxonomy, which involves identification, classification, and nomenclature of organisms.
2. Taxonomic classification categories arrange species in a hierarchical order from domain to genus. Identification techniques include microscopy, culture characteristics, biochemical tests, and nucleic acid analysis.
3. Bacteria can be classified by morphology, staining, culture characteristics, oxygen requirements, metabolism, and environmental tolerances. Cocci, bacilli, vibrios, spirochetes, and spirilla are morphological groups.
This document provides information on bacteria morphology and identification. It discusses that bacteria are microscopic, unicellular organisms that can perform essential life functions. It describes different bacterial shapes including cocci, bacilli, vibrios, spirilla, and spirochaetes. Gram staining is used to classify bacteria as either gram positive or gram negative. Common gram positive cocci like staphylococci and streptococci are examined in detail. Requirements for bacterial growth such as nutrients, oxygen, temperature, and pH are also reviewed.
This document discusses the classification of microorganisms. It describes the three domain system proposed by Carl Woese which divides organisms into Archaea, Bacteria and Eukarya. It then provides details on the characteristics of fungi, algae, protozoa, viruses and bacteria; and discusses methods used to identify bacteria including biochemical tests and serological tests.
This document summarizes R.H. Whittaker's five kingdom classification system, which includes the kingdoms of Monera, Protista, Fungi, Plantae, and Animalia.
[1] Kingdom Monera includes bacteria, which are unicellular prokaryotes found everywhere that lack nuclei and organelles. They can be autotrophic through photosynthesis or chemosynthesis, or heterotrophic through parasitism or saprophytism.
[2] Kingdom Protista contains unicellular eukaryotic organisms that are autotrophic or heterotrophic, including diatoms, algae, dinoflagellates, and protozoa.
[3
Bacteria are microbes with a cell structure simpler than that of many other organisms. Their control centre, containing the genetic information, is contained in a single loop of DNA. Some bacteria have an extra circle of genetic material called a plasmid rather than a nucleus. The plasmid often contains genes that give the bacterium some advantage over other bacteria. For example it may contain a gene that makes the bacterium resistant to a certain antibiotic.
Bacteria are classified into five groups according to their basic shapes: spherical (cocci), rod (bacilli), spiral (spirilla), comma (vibrios) or corkscrew (spirochaetes). They can exist as single cells, in pairs, chains or clusters.
Bacteria are unicellular prokaryotic organisms that are found everywhere and are very abundant. They can thrive in extreme conditions where other organisms cannot live. Bacterial cells are typically much smaller than human cells. Bacteria come in a variety of shapes including spherical (cocci), rod-shaped (bacilli), spiral, and comma-shaped. The shape of a bacterial cell is an important characteristic that is specific to its species and can affect its pathogenicity, motility, and other traits. Common bacterial shapes include cocci arranged in pairs, chains, and clusters, as well as rod-shaped bacilli arranged singly or attached in pairs or chains.
The documents discuss the Kingdom Eubacteria, which contains unicellular prokaryotes that reproduce by binary fission. Eubacteria are classified by their gram staining and include four major phyla: Cyanobacteria, which are photosynthetic; Spirochetes, which have a spiral shape and can cause diseases; and Gram-positive bacteria, which differ from Gram-negative bacteria in their cell wall composition and antibiotic susceptibility. The documents explore the structural features and functions of Eubacteria as well as methods for identifying and classifying them.
A. Protists are a diverse group of unicellular or multicellular eukaryotic organisms that include important pathogens. B. Helminth parasites like roundworms and flatworms are often identified microscopically and can infect the intestines or other tissues. C. Fungi are eukaryotic organisms with chitin cell walls that can be unicellular or multicellular, including medically important molds, yeasts, and dermatophytes. D. Algae include unicellular and multicellular photosynthetic protists used to produce industrial compounds like agar. E. Lichens are a symbiotic partnership between fungi and algae or cyanobacteria that
MICROBIOLOGY QUICK LEARNFood MicrobiologyBACTERIA- Cultural Characteristics...Saajida Sultaana
Bacteria are important in food microbiology. They can cause food spoilage and illness, but some species are beneficial. Bacteria have specific nutrient and environmental needs. Their cultural characteristics include morphology, encapsulation, endospores, and cell aggregates. Morphological observation identifies size, shape, and structures. Encapsulation and endospores help bacteria survive harsh conditions. Some bacteria form chains or clumps. Their growth produces chemical changes and discolors or textures food. Understanding bacterial growth factors is key to food preservation and preventing spoilage.
Bacteria are classified in several ways:
1. By staining (Gram positive/negative, acid-fast), shape (cocci, bacilli), motility, environment (aerobic/anaerobic).
2. The bacterial cell has a cell wall, cell membrane, flagella/fimbriae and cytoplasm. The cell wall provides structure and protection through its peptidoglycan layer.
3. Bacteria are further classified based on nutrition sources, temperature, pH and salt tolerance ranges they thrive in. Most bacteria serve important ecological roles while some can cause disease.
This document provides information about biology and the classification of living organisms. It discusses the following key points:
- Biology is the science of living organisms and life processes. Modern biology integrates with other fields like chemistry and physics.
- Characteristics of living things include growth, reproduction, metabolism, response to stimuli, homeostasis, and evolution.
- Organisms are classified and grouped into a hierarchy of taxa including species, genus, family, order, class, phylum, and kingdom.
- The five kingdom system classifies organisms into Monera, Protista, Fungi, Plantae, and Animalia based on characteristics like cell structure, nutrition, and lifestyle. Examples of groups within each
This document provides an introduction and overview of gram-negative bacteria. It discusses their key characteristics and classification. Specifically, it summarizes several genera of gram-negative bacteria, including Pseudomonas, Xanthomonas, Azotobacter, Rhizobium, Methylococcus, Acetobacter, and Legionella. It also describes the families they belong to, such as Pseudomonadaceae, Azotobacteraceae, and Legionellaceae.
- Microorganisms play key roles in human health, agriculture, food production, and the environment. They can cause infectious diseases but have also helped control diseases through vaccines and antibiotics. Microbes aid agriculture through nitrogen fixation and by enabling ruminant digestion. They are crucial to food industries like dairying and brewing through fermentation. Some microbes also produce biofuels like methane and ethanol. Overall, microorganisms both threaten and greatly benefit human lives and activities.
Prokaryotes include bacteria and archaea. Bacteria were first observed in 1674 and include diverse species found in many habitats. Prokaryotes are single-celled without internal membranes and reproduce through binary fission. Major groups include eubacteria like E. coli and archaea found in extreme environments like hot springs or salt lakes. Bacteria play important roles in ecosystems through processes like nitrogen fixation and photosynthesis.
Similar to THE GENERAL PROPERTIES OF PROTEOBACTERIA AND ITS TYPES (20)
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
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Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
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Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
2. INTRODUCTION
• The phylum Proteobacteria is the largest, phylogenetically coherent bacterial
group with over 2,000 species assigned to more than 500 genera.
• Many of these gram-negative bacteria are of considerable importance, either as
disease agents or because of their contributions to ecosystems. In addition,
bacteria such as Escherichia coli, are major experimental organisms studied in
many laboratories.
• These bacteria are very diverse in their metabolism and life-styles, which range
from obligate intracellular parasitism to a free-living existence in soil and
aquatic habitats.
• They could be Chemolithotrophic /Photoautotrophs/ chemolithotrophs /
chemoheterotrophs
• Some Proteobacteria produce specialized structures such as prosthecae, stalks,
buds, sheaths, or complex fruiting bodies.
• They depend on the prey’s or host’s energy supply and/or cell constituents.
3. GENERAL CHARACTERISTICS
• The phylum (Proteobacteria) belongs to the domain Bacteria and is
comprised of gram-negative bacteria with an outer membrane
consisting largely of lipopolysaccharides.
• Many of them have flagella used for locomotion. Few of them move
through bacterial gliding; others are non-motile.
• Members of this phylum are anaerobic. Many of which are
facultative anaerobes; others are obligate aerobes.
• The name of the phylum is named after the Greek god of the sea,
Proteus, who is regarded as a god capable of assuming different
shapes.
• This is because of the great diversity of forms of species belonging to
this phylum.
4. CONTD
• Volume 2 of the second edition
of Bergey’s Manual is devoted
entirely to the proteobacteria.
• Although 16S rRNA studies
show that they are
phylogenetically related,
proteobacteria vary markedly
in many aspects.
• The morphology of these gram-
negative bacteria ranges from
simple rods and cocci to genera
with prosthecae, buds, and
even fruiting bodies.
6. • 1. PURPLE NON-SULPHUR BACTERIA-
(Rhodospirillum and Azospirillum)
• RICKETTSIA
• NITRIFYING BACTERIA
CLASS ALPHA PROTEOBACTERIA
7. CLASS
ALPHA
PROTEOBACTERIA
• The Alpha proteobacteria
include most of the
oligotrophic proteobacteria
(those capable of growing at
low nutrient levels).
• Some have unusual
metabolic modes such as
methylotrophy
(Methylobacterium),
chemolithotrophy
(Nitrobacter), and the ability
to fix nitrogen (Rhizobium).
Contains seven orders and 20 families.
8. 1. PURPLE NON-SULPHUR BACTERIA-
(Rhodospirillum and Azospirillum)
• All purple nonsulfur bacteria are alpha-proteobacteria, with the exception of
Rhodocyclus (proteobacteria).
• The purple nonsulfur bacteria are exceptionally flexible in their choice of an
energy source. Normally they grow anaerobically as photoorganoheterotrophs;
they trap light energy and employ organic molecules as both electron and carbon
sources.
• In the absence of light, most purple nonsulfur bacteria can grow aerobically as
chemoorganoheterotrophs, but some species carry out fermentations
anaerobically.
• Although they are called nonsulfur bacteria, some species can oxidize very low,
nontoxic levels of sulfide to sulfate, but they do not oxidize elemental sulfur to
sulfate.
• Oxygen inhibits bacteriochlorophyll and carotenoid synthesis so that cultures
growing aerobically in the dark are colorless.
9. 2. RICKETTSIA
• Belong to the family
Rickettsiaceae of the alpha-
proteobacteria.
• These bacteria are rod-shaped,
coccoid, or pleomorphic with
typical gram-negative walls and
no flagella.
• Although their size varies, they
tend to be very small, is 0.3 to 0.5
micrometer in diameter and 0.8
to 2.0 micrometer long;
• All species are parasitic or
mutualistic.
10. 3. NITRIFYING BACTERIA
In Bergey’s Manual, the chemolithotrophic bacteria are distributed between the alpha,
beta, and gamma-proteobacteria. The nitrifying bacteria are found in all three classes.
• Nitrobacter -aplha-proteobacteria
• Nitrosomonas and Nitrosospira- ᵞ-proteobacteria;
• Nitrococcus,- ᵞ -proteobacteria;
• Nitrosococcus - ᵞ -proteobacteria.
• All are aerobic, gram negative organisms with the ability to capture energy from the
oxidation of either ammonia or nitrite. However, they differ considerably in other
properties .
• Nitrifiers may be rod-shaped, ellipsoidal, spherical, spirillar or lobate, and they may
possess either polar or peritrichous flagella . Often they have extensive membrane
complexes in their cytoplasm.
• Identification is based on properties such as their preference for nitrite or ammonia,
their general shape, and the nature of any cytomembranes present.
11. • Nitrifying bacteria make important contributions to the nitrogen cycle.
Seen in soil, sewage disposal systems, and freshwater and marine
habitats.
• In the same niches, members of the gamma-proteobacterial genus
Nitrococcus then oxidize nitrite to nitrate.
• The whole process of converting ammonia to nitrite to nitrate is called
nitrification and it occurs rapidly in oxic soil treated with fertilizers
containing ammonium salts.
• Nitrate is readily used by plants, but it is also rapidly lost through
leaching of water-soluble nitrates and by denitrification to nitrogen
gas, so the benefits gained from nitrification can be fleeting.
12.
13. CLASS BETAPROTEOBACTERIA
• The BETA-proteobacteria overlap the
ALPHA-proteobacteria metabolically but
tend to use substances that diffuse from
organic decomposition in the anoxic zone
of habitats. Some of these bacteria use
hydrogen, ammonia, methane, volatile
fatty acids, and similar substances.
• Beta-proteobacteria may be
chemoheterotrophs, photolithotrophs,
methylotrophs, and chemolithotrophs.
• The class Betaproteobacteria has seven
orders and 12 families.
14. • Contains Thiobacillus
like Nitrifying bacteria
and Colorless sulfur
bacteria
• Unicellular
• Rod shaped/spiral shaped
• Sulphur oxidizing
bacteria
• Non motile/ motile by
flagella
Example: Thiobacillus and
Macromonas
Order Hydrogenophilales Order Neisseriales
• nonmotile, aerobic,
gram-negative cocci
• have capsules and
fimbriae
• Chemoorganotrophic
• positive and catalase
positive
Example: Neisseria
gonorrhoeae
Order Nitrosomonadales
• Chemolithotrophs
• Nitrifying bacteria
Example:
Nitrosomonas and
Nitrosospira
15.
16. CLASS GAMMAPROTEOBACTERIA
• The gamma-proteobacteria constitute the
largest subgroup of proteobacteria with
an extraordinary variety of physiological
types. Many important genera are
chemoorganotrophic and facultatively
anaerobic.
• Other genera contain aerobic
chemoorganotrophs, photolithotrophs,
chemolithotrophs, or methylotrophs.
Phylogenetic Relationships among gamma- Proteobacteria
17. THE PURPLE SULFUR BACTERIA
• The purple photosynthetic bacteria are distributed between three
subgroups of the proteobacteria.
• Most of the purple nonsulfur bacteria are gamma-proteobacteria.
Because the purple sulfur bacteria are gamma-proteobacteria.
• Purple sulfur bacteria are strict anaerobes and usually
photolithoautotrophs.
• They oxidize hydrogen sulfide to sulfur and deposit it internally as
sulfur granules (usually within invaginated pockets of the plasma
membrane); often they eventually oxidize the sulfur to sulfate.
• Hydrogen also may serve as an electron donor. Thiospirillum,
Thiocapsa, and Chromatium are typical purple sulfur bacteria.
18. CLASS DELTAPROTEOBACTERIA
• Although the -proteobacteria are not a
large assemblage of genera, they show
considerable morphological and
physiological diversity. These bacteria can
be divided into two general groups, all of
them chemoorganotrophs.
• Some genera are predators such as the
bdellovibrios and myxobacteria. Others
are anaerobes that generate sulfide from
sulfate and sulfur while oxidizing organic
nutrients. The class has eight orders and
20 families
19.
20. EXAMPLE: Order Myxococcales- MYXOBACTERIA
• Myxobacteria are gram-negative, aerobic soil bacteria characterized by gliding
motility, a complex life cycle with the production of fruiting bodies, and the
formation of dormant myxospores.
• In addition, their G C content is around 67 to 71%, significantly higher than that
of most gliding bacteria. Myxobacterial cells are rods, about 0.4 to 0.7 by 2 to 8
MICROm long, and may be either slender with tapered ends or stout with rounded,
blunt ends.
• The order Myxococcales is divided into six families based on the shape of vegetative
cells, myxospores, and sporangia
• The myxobacterial life cycle is quite distinctive and in many ways resembles that of
the cellular slime molds. In the presence of a food supply, myxobacteria migrate
along a solid surface, feeding and leaving slime trails.
• During this stage the cells often form a swarm and move in a coordinated fashion.
Some species congregate to produce a sheet of cells that moves rhythmically to
generate waves or ripples. When their nutrient supply is exhausted, the
myxobacteria aggregate and differentiate into a fruiting body.
21.
22. CLASS EPSILONPROTEOBACTERIA
• In the second edition of Bergey’s Manual is a result of the recent isolation
of two genera of moderately thermophilic (optimum growth temperature
about 55°C) chemolithoautotrophs from deep-sea hydrothermal vents.
• Members of the genera Nautilia and Caminibacter are strict anaerobes
that oxidize H2 and use sulfur as an electron acceptor. Species are found
as either freely living or as symbionts of vent macrofauna.
• Slender
• Gram Negative rods
• Helical/vibrioid
• Two important genera
are Campylobacter
and Helicobacter
23. • The EPSILON-proteobacteria are the smallest of the five
proteobacterial classes. They all are slender gram-negative rods,
which can be straight, curved, or helical.
• The EPSILON-proteobacteria have one order, Campylobacterales,
and three families: Campylobacteraceae, Helicobacteraceae, and the
recently added Nautiliaceae.
• Two pathogenic genera, Campylobacter and Helicobacter, are
microaerophilic, motile, helical or vibrioid, gram-negative rods.
• The genus Campylobacter contains both nonpathogens and species
pathogenic for humans and other animals. C. fetus causes
reproductive disease and abortions in cattle and sheep.
• It is associated with a variety of conditions in humans ranging from
septicemia (pathogens or their toxins in the blood) to enteritis
(inflammation of the intestinal tract). C. jejuni causes abortion in
sheep and enteritis diarrhea in humans
24. contd
• There are at least 23 species of Helicobacter, all isolated from the stomachs and
upper intestines of humans, dogs, cats, and other mammals. Most infections are
probably acquired during childhood, but the precise mode of transmission is
unclear.
• The major human pathogen is Helicobacter pylori, which causes gastritis and
peptic ulcer disease. H. pylori produces large quantities of urease, and urea
hydrolysis appears to be associated with its virulence.
• The genomes of C. jejuni and H. pylori (both about 1.6 million base pairs in size)
have been sequenced. They are now being studied and compared in order to
understand the life styles and pathogenicity of these bacteria.The
e-proteobacteria are now recognized to be more metabolically and ecologically
diverse than previously thought. For instance, filamentous microbial mats in
anoxic, sulfide-rich cave springs are dominated by members of the
-proteobacteria).