This document summarizes a study that analyzed ancient and modern tuatara DNA to estimate molecular evolutionary rates in this species. The key points are:
- Tuatara are considered "living fossils" that have changed little morphologically since the Cretaceous period. However, the study found tuatara have the highest rate of molecular change recorded in vertebrates based on an analysis of tuatara mitochondrial DNA.
- The study estimated tuatara molecular evolutionary rates using Bayesian statistics and sequencing DNA from sub-fossil tuatara bones ranging from 650 to 8,750 years old.
- Surprisingly, the estimated rate of 1.56 substitutions per nucleotide per million years in tuat
This document discusses a study that analyzed thousands of non-coding human accelerated regions (ncHARs) that have accumulated mutations more rapidly in humans compared to chimpanzees since their divergence. The researchers predicted that at least 30% of ncHARs function as developmental enhancers based on sequence analysis, evolutionary history, epigenetic marks, and transcription factor binding sites. They tested 29 prioritized ncHARs as developmental enhancers in transgenic mice and found that 24 drove expression in embryonic tissues, with 17 showing consistent expression patterns. Five ncHAR enhancers exhibited potential differences in activity between the human and chimpanzee sequences.
This study analyzed genetic diversity and population structure of the striped snakehead fish (Channa striata) across populations in Malaysia and Sumatra, Indonesia using mitochondrial DNA analysis. Twenty-five populations totaling 345 individuals were sampled and divided into six regions based on physiogeography. High genetic diversity was found in four populations, suggesting they could be good candidates for selective breeding programs. Two major phylogenetic lineages were detected, separated by the Bintang Mountain Range. Most population pairs showed significant genetic differentiation, though some distant populations were closely related likely due to ancient dispersal and human translocation. The findings provide an important basis for conservation and selective breeding of genetically distinct populations.
1) Transgenic fish models carrying bacteriophage λ and plasmid pUR288 vectors were developed to improve methods for assessing health risks from environmental mutagens and establish new animal models for studying in vivo mutagenesis.
2) The bacteriophage λ transgenic medaka model uses the cII and lacI genes as mutational targets, allowing detection of mutations through packaging of the phage vector and infection of E. coli. Spontaneous mutation frequencies in medaka were comparable to rodent models.
3) Exposure to chemical mutagens like ENU induced concentration-dependent, tissue-specific, and time-dependent increases in cII mutations, demonstrating the utility of the transgenic fish model for studying mut
4-IJF-Studies on fresh milt-Indian J. Fish.63(1) 67-73 2016Ravindragouda Patil
This document summarizes a study on the fresh milt parameters and cellular changes during cryopreservation of spermatozoa from the endangered Deccan mahseer fish. Physico-chemical analysis of fresh milt found a sperm density of 3.93±0.11 x 107 spermatozoa/ml and spermatocrit value of 67.08±1.22%. Ultrastructure analysis by electron microscopy showed fresh spermatozoa had a spherical head, small midpiece with mitochondria, and long tail, while cryopreserved spermatozoa showed loosening of chromatin and disrupted membranes. Nitroblue tetrazolium assays also indicated lower mitochondrial enzyme activity in cryopreserved
Animal breeding is a process that is being used from many years ago. In the earlier days, the breeders use to increase the qualities in the animals by using breeding and other methods. But by the invention of the molecular techniques, it is become easier to manipulate any animal and to enhance the traits or different qualities in the animals. In this regard, different methods have used these methods are discussed in this article. The animal transgenesis is used for different purposes such as in research purposes, like organ transplant source for humans, as protein extraction sources, as drug extraction process, in hormones production, and in many other purposes.
A systematic, data driven approach to the combined analysis of microarray and...Laurence Dawkins-Hall
The use of gene expression data from Micro arrays coupled with WT QTL's linked to Tryp resistance phenotypes in Cattle to elucidate pertinent genetic changes underpinning phenotype in putative candidate genes
Kate L Hertweck is an evolutionary biologist and bioinformaticist who uses genomic data to study evolution in monocots and identify cancer biomarkers. She has studied monocot phylogenetics using multiple loci, identified transposable element content in monocots which does not correlate with genome size, and found parallel responses to selection for development time in experimental Drosophila populations including differences in transposable element load and heterozygosity between treatments. Her cancer research with collaborators uses mitochondrial variants to study prostate cancer and somatic mutations to inform head and neck cancer biomarker studies. She emphasizes that bioinformatic skills are transferable among model systems and integrating genomic and experimental data provides insights into evolution and disease
1) Mature dendritic cells project dendrite-like protrusions that allow them to scan a larger area than their cell body.
2) Upon initial contact with a T cell via a dendrite, dendritic cells project numerous mobile membrane extensions and migrate their cell body toward the T cell to tightly entangle it.
3) Using time-lapse microscopy and two-photon imaging of lymph nodes, the study observed dendritic cells polarizing membrane extensions and migrating toward T cells after initial dendrite-mediated contact, before tight conjugation.
This document discusses a study that analyzed thousands of non-coding human accelerated regions (ncHARs) that have accumulated mutations more rapidly in humans compared to chimpanzees since their divergence. The researchers predicted that at least 30% of ncHARs function as developmental enhancers based on sequence analysis, evolutionary history, epigenetic marks, and transcription factor binding sites. They tested 29 prioritized ncHARs as developmental enhancers in transgenic mice and found that 24 drove expression in embryonic tissues, with 17 showing consistent expression patterns. Five ncHAR enhancers exhibited potential differences in activity between the human and chimpanzee sequences.
This study analyzed genetic diversity and population structure of the striped snakehead fish (Channa striata) across populations in Malaysia and Sumatra, Indonesia using mitochondrial DNA analysis. Twenty-five populations totaling 345 individuals were sampled and divided into six regions based on physiogeography. High genetic diversity was found in four populations, suggesting they could be good candidates for selective breeding programs. Two major phylogenetic lineages were detected, separated by the Bintang Mountain Range. Most population pairs showed significant genetic differentiation, though some distant populations were closely related likely due to ancient dispersal and human translocation. The findings provide an important basis for conservation and selective breeding of genetically distinct populations.
1) Transgenic fish models carrying bacteriophage λ and plasmid pUR288 vectors were developed to improve methods for assessing health risks from environmental mutagens and establish new animal models for studying in vivo mutagenesis.
2) The bacteriophage λ transgenic medaka model uses the cII and lacI genes as mutational targets, allowing detection of mutations through packaging of the phage vector and infection of E. coli. Spontaneous mutation frequencies in medaka were comparable to rodent models.
3) Exposure to chemical mutagens like ENU induced concentration-dependent, tissue-specific, and time-dependent increases in cII mutations, demonstrating the utility of the transgenic fish model for studying mut
4-IJF-Studies on fresh milt-Indian J. Fish.63(1) 67-73 2016Ravindragouda Patil
This document summarizes a study on the fresh milt parameters and cellular changes during cryopreservation of spermatozoa from the endangered Deccan mahseer fish. Physico-chemical analysis of fresh milt found a sperm density of 3.93±0.11 x 107 spermatozoa/ml and spermatocrit value of 67.08±1.22%. Ultrastructure analysis by electron microscopy showed fresh spermatozoa had a spherical head, small midpiece with mitochondria, and long tail, while cryopreserved spermatozoa showed loosening of chromatin and disrupted membranes. Nitroblue tetrazolium assays also indicated lower mitochondrial enzyme activity in cryopreserved
Animal breeding is a process that is being used from many years ago. In the earlier days, the breeders use to increase the qualities in the animals by using breeding and other methods. But by the invention of the molecular techniques, it is become easier to manipulate any animal and to enhance the traits or different qualities in the animals. In this regard, different methods have used these methods are discussed in this article. The animal transgenesis is used for different purposes such as in research purposes, like organ transplant source for humans, as protein extraction sources, as drug extraction process, in hormones production, and in many other purposes.
A systematic, data driven approach to the combined analysis of microarray and...Laurence Dawkins-Hall
The use of gene expression data from Micro arrays coupled with WT QTL's linked to Tryp resistance phenotypes in Cattle to elucidate pertinent genetic changes underpinning phenotype in putative candidate genes
Kate L Hertweck is an evolutionary biologist and bioinformaticist who uses genomic data to study evolution in monocots and identify cancer biomarkers. She has studied monocot phylogenetics using multiple loci, identified transposable element content in monocots which does not correlate with genome size, and found parallel responses to selection for development time in experimental Drosophila populations including differences in transposable element load and heterozygosity between treatments. Her cancer research with collaborators uses mitochondrial variants to study prostate cancer and somatic mutations to inform head and neck cancer biomarker studies. She emphasizes that bioinformatic skills are transferable among model systems and integrating genomic and experimental data provides insights into evolution and disease
1) Mature dendritic cells project dendrite-like protrusions that allow them to scan a larger area than their cell body.
2) Upon initial contact with a T cell via a dendrite, dendritic cells project numerous mobile membrane extensions and migrate their cell body toward the T cell to tightly entangle it.
3) Using time-lapse microscopy and two-photon imaging of lymph nodes, the study observed dendritic cells polarizing membrane extensions and migrating toward T cells after initial dendrite-mediated contact, before tight conjugation.
This document summarizes research characterizing MHC class I alleles and haplotypes in sooty mangabeys using deep sequencing techniques. 121 classical and non-classical MHC class I alleles were identified in 165 sooty mangabeys. 22 haplotypes consisting of combinations of Ceat-A and Ceat-B alleles were also determined. This characterization of MHC class I alleles and haplotypes in sooty mangabeys provides a valuable resource for studying cellular immunity in these natural SIV hosts.
"Estimation of Divergence Times in Asparagales in the Presence of Hybridization," presented in symposium "Insights and Benefits from Monocot Palaeobiology: Fossils, DNA, and Phylogenies" at Monocots V (5th International Conference on Comparative Biology of Monocotyledons, The New York Botanical Garden, July 2013).
This document describes the development of an interspecies tiling array to analyze the transgenic genome of mice that were engineered to express the human protamine domain. Key points:
1) A single copy of the human protamine domain was randomly inserted into the genome of mice. Expression of the transgene recapitulated normal human levels without disrupting endogenous gene expression.
2) An interspecies tiling array was designed to simultaneously analyze the orthologous protamine domains in mouse and human. Probe design accounted for repetitive elements to allow comparison of highly similar sequences.
3) Initial results demonstrate the array can provide parallel analysis of orthologous sequences from different species, serving as a valuable tool for interrogating transgenic
Knockout mouse model of Pompe Disease(Group 8)Sindu09
1. Researchers generated a knockout mouse model of Pompe disease by disrupting the murine acid α-glucosidase gene (Gaa). Mice with this gene knockout (Gaa-/-) lacked acid α-glucosidase and accumulated glycogen in their lysosomes, mimicking the disease.
2. Comparison of different mouse models found that disruption of exon 13 represented the infantile form, while disruption of exon 6 represented both infantile and adult forms, showing varying degrees of weakness and glycogen storage.
3. Future research includes developing new recombinant enzymes and investigating alternative treatment approaches, such as suppressing the starch binding domain-containing protein 1 gene along with acid α-glucosidase.
This study evaluated the accuracy of nine programs for predicting the topological structure of integral membrane transport proteins. The programs were first tested on four families of secondary carriers with known topologies, finding SPOCTOPUS, MEMSAT, and HMMTOP to be most accurate. These three programs were then used to analyze larger groups of channels and carriers from various families and subclasses. The results provide guidance on the relative performance of prediction programs for different types of transport proteins, as well as insights into the topological characteristics of various families and evolutionary relationships.
This document discusses a study that found molecular and morphological evidence suggesting that the flagellate Ancyromonas is closely related to the common ancestor of metazoans, fungi, and choanoflagellates. Analyses of 18S rRNA gene sequences from major eukaryotic lineages using maximum likelihood, minimum evolution, and maximum parsimony supported Ancyromonas forming its own lineage, called Ancyromonadida, that is more closely related to opisthokonts than its nearest protist relatives. However, low bootstrap support for deep nodes limits the ability of 18S rDNA to fully resolve this aspect of eukaryotic phylogeny.
The document reports on a study that identified quantitative trait loci (QTLs) associated with stigma exertion rate and spikelet number per panicle in rice. Eight QTLs for single stigma exertion, double stigma exertion, and total stigma exertion were detected on chromosomes 6, 10, 11 and three QTLs for spikelet number per panicle were identified on chromosomes 1 and 3. One QTL for spikelet number was detected in two different environments. The study provides information to aid in fine mapping, gene cloning and marker-assisted selection for improving hybrid rice seed production.
This study investigates the population of bluntnose sixgill sharks (Hexanchus griseus) in the Central Mediterranean Sea, particularly around the Maltese Islands. Over 435 sharks were sampled between 2004-2008 from a fish market in Malta. Samples were collected and recorded for weight, length, sex, and location. Genetic analysis of tissue samples is being conducted to study population structure using mtDNA and microsatellites. Preliminary results show sizes of sampled sharks, with no gravid females found. The aim is to use genetic and morphological data to understand the species' regional status and inform fishery management.
Genomic gene expression changes resulting from Trypanosomiasis: a horizontal study Examining expression changes elucidated by micro arrays in seminal tissues associated with the pathophysiology of Trypanosomiasis during disease progression
Molecular characterization of rice (Oryza sativa L.) genotypes using target r...Innspub Net
In the present investigation, based on the seven rice putative candidate iron transporter genes, novel TRAP markers were developed. These markers were successfully employed in the molecular diversity study among 30 rice genotypes representing improved rice cultivars and land races with varied grain iron content (7.38 - 30.58 ppm). Totally, thirty TRAP primer combinations were screened, which generated 703 bands out of which 654 were polymorphic (93%) with an average of 21.8 bands per primer combination. The average polymorphic information content (PIC) values ranged from 0.09 (Osysl4b+ME05) to 0.25 (Osnramp5c+ME05, Osnramp1b+ME02 and Osysl4a +ME02). Gene diversity (H ˆ
) ranged from 0.10 (Osysl4b+ME05) to 0.31 (Osnramp1b + ME02 and Osysl4a +ME02). The Jaccard dissimilarity ranged from 0.15 to 0.52, explaining 37% of genetic variation (Table 4). Grouping of genotypes based on UPGMA and principal coordinate analysis (PCoA) were found comparable and grouping of genotypes into a different cluster was found mainly on the basis of pedigree relationships. TRAP markers revealed well resolved relationships among rice genotypes. The information generated from this study will helps to select parental combinations for breeding high iron content
rice varieties.
1) The study investigated the effects of the tyrosine kinase inhibitors crizotinib and dasatinib on canine osteosarcoma cell lines. It found that dasatinib more effectively suppressed cell viability and inhibited hepatocyte growth factor-induced invasion and migration compared to crizotinib.
2) Exogenous hepatocyte growth factor increased invasion, migration, and matrix metalloproteinase production in the osteosarcoma cell lines.
3) Preliminary results showed that four dogs with osteosarcoma treated with adjuvant dasatinib therapy experienced an apparent clinical benefit.
The Effects of Genetic Alteration on Reprogramming of Fibroblasts into Induc...remedypublications2
Induced Pluripotent Stem Cells (iPSCs) can be generated from somatic cells by ectopic expression of
Yamanaka factors (
Oct4
,
Sox2
,
Klf4
and
c-Myc
) or combination of other factors. Genetic alteration
of fibroblasts exhibits an effect on reprogramming efficiency through multiple signaling pathways,
including epigenetic modifications, metabolic shifts, Mesenchymal-To-Epithelial Transition
(MET) and cell proliferation. In order to better understand the underlying mechanisms in cell fate
determination, in this review we will summarize several genetic alterations involved in the regulation
of reprogramming fibroblasts into iPSCs.
This document summarizes the mapping of genetic sequences disclosed in patents onto the maize, rice, soybean, and human genomes. The key findings are:
- 2.8 million patent sequences were mapped to each of the maize and soybean genomes, and 2.5 million to the rice genome, compared to 31 million mapped to the human genome.
- Less than 0.3% of mapped sequences for plant genomes were referenced in patent claims, compared to over 1% for the human genome.
- Over 80% of sequences mapped to plant genomes overlapped with sequences from other genomes, including the human genome. Only 12% of human sequences overlapped with plant genomes.
- 3,
Pells et al [2015] PLoS ONE 10[7] e0131102Steve Pells
This research article identifies novel human embryonic stem cell regulators based on their conserved and distinct CpG island methylation patterns. The researchers analyzed CpG island methylation in four human embryonic stem cell lines using a CpG island array and identified 1,111 CpGs that were methylated in all stem cell lines. They compared the methylation profiles to somatic tissues and mRNA expression data to identify stem cell-specific methylation patterns associated with gene expression. Genes related to transcriptional repression and activation were overrepresented among genes associated with methylated or unmethylated CpGs specifically in stem cells. Knockdown experiments confirmed that some candidate regulators induced stem cell differentiation, while overexpression modulated induced pluripotent stem cell formation
The document reviews protocols for generating induced pluripotent stem cells (iPSCs) including choice of reprogramming factors, delivery methods, and target cell types. The core reprogramming factors are Oct4, Sox2, Klf4, and c-Myc, though variations exist. Initial methods used integrating viruses but newer approaches aim to be non-integrating. Fibroblasts are commonly used as starting cells but iPSCs have been made from other cell types. Standardization of parameters can improve comparisons between experiments.
This document describes the development of a multiplex PCR assay targeting the cgcA gene, which encodes a diguanylate cyclase, to differentiate between species within the genus Cronobacter. Analysis of 12 Cronobacter genomes identified 7 conserved diguanylate cyclase-encoding genes, one of which, cgcA, showed species-specific divergence that matched known phylogenetic relationships between Cronobacter species. Primers were designed for this gene and tested in a multiplex PCR assay on 305 Cronobacter isolates representing 6 species. The assay correctly identified the species of all isolates tested and did not identify any of 20 non-Cronobacter species, demonstrating high specificity and sensitivity for rapid identification of Cronobacter.
This study assessed the effects of three centrifugal forces (600×g, 3000×g, and 6000×g for 10 minutes at room temperature) on ram sperm motility and functionality. Higher centrifugal forces resulted in greater sperm packaging but also had deleterious effects on sperm quality. Centrifugation at 3000×g and 6000×g impaired sperm movement patterns after 2 hours of incubation at 37°C compared to lower forces. While viability was not significantly different between groups, apoptotic sperm increased in the 6000×g samples immediately after centrifugation. The researchers concluded that centrifugal forces of 3000×g or greater induced harmful effects on ram sperm quality, and lower forces did not provide adequate sperm packaging.
CRISPR as a potential tool for malaria eradicationMatthias Samwald
Why avoiding delays to gene-drive based mosquito eradication should be the most important goal of the global community right now, and why it is not.
Presentation at the Vienna Rationality Meetup 14.05.2016
Este documento discute a necessidade de repensar a educação para promover o desenvolvimento sustentável em um mundo complexo. Defende uma abordagem humanista da educação que promova a inclusão, a justiça social e os direitos humanos. Também destaca a importância de considerar contextos locais e sistemas de conhecimento diversos ao formular políticas educacionais globais e locais.
Individual and demographic consequences of reduced body condition following r...João Soares
Repeated exposure to high temperatures (≥35°C) negatively impacted the body condition of White-plumed Honeyeaters, but only in dry conditions with low rainfall. Males with reduced body condition after heat exposure were less likely to be recaptured the following spring, suggesting higher mortality. Females and smaller individuals showed lower survival after heat exposure due to their smaller size. Over time, as maximum temperatures increased and rainfall declined, annual survival of the honeyeaters declined as well. Repeated exposure to heat stress may have contributed to increases in the average body size of the population by reducing survival of smaller birds.
This document summarizes research characterizing MHC class I alleles and haplotypes in sooty mangabeys using deep sequencing techniques. 121 classical and non-classical MHC class I alleles were identified in 165 sooty mangabeys. 22 haplotypes consisting of combinations of Ceat-A and Ceat-B alleles were also determined. This characterization of MHC class I alleles and haplotypes in sooty mangabeys provides a valuable resource for studying cellular immunity in these natural SIV hosts.
"Estimation of Divergence Times in Asparagales in the Presence of Hybridization," presented in symposium "Insights and Benefits from Monocot Palaeobiology: Fossils, DNA, and Phylogenies" at Monocots V (5th International Conference on Comparative Biology of Monocotyledons, The New York Botanical Garden, July 2013).
This document describes the development of an interspecies tiling array to analyze the transgenic genome of mice that were engineered to express the human protamine domain. Key points:
1) A single copy of the human protamine domain was randomly inserted into the genome of mice. Expression of the transgene recapitulated normal human levels without disrupting endogenous gene expression.
2) An interspecies tiling array was designed to simultaneously analyze the orthologous protamine domains in mouse and human. Probe design accounted for repetitive elements to allow comparison of highly similar sequences.
3) Initial results demonstrate the array can provide parallel analysis of orthologous sequences from different species, serving as a valuable tool for interrogating transgenic
Knockout mouse model of Pompe Disease(Group 8)Sindu09
1. Researchers generated a knockout mouse model of Pompe disease by disrupting the murine acid α-glucosidase gene (Gaa). Mice with this gene knockout (Gaa-/-) lacked acid α-glucosidase and accumulated glycogen in their lysosomes, mimicking the disease.
2. Comparison of different mouse models found that disruption of exon 13 represented the infantile form, while disruption of exon 6 represented both infantile and adult forms, showing varying degrees of weakness and glycogen storage.
3. Future research includes developing new recombinant enzymes and investigating alternative treatment approaches, such as suppressing the starch binding domain-containing protein 1 gene along with acid α-glucosidase.
This study evaluated the accuracy of nine programs for predicting the topological structure of integral membrane transport proteins. The programs were first tested on four families of secondary carriers with known topologies, finding SPOCTOPUS, MEMSAT, and HMMTOP to be most accurate. These three programs were then used to analyze larger groups of channels and carriers from various families and subclasses. The results provide guidance on the relative performance of prediction programs for different types of transport proteins, as well as insights into the topological characteristics of various families and evolutionary relationships.
This document discusses a study that found molecular and morphological evidence suggesting that the flagellate Ancyromonas is closely related to the common ancestor of metazoans, fungi, and choanoflagellates. Analyses of 18S rRNA gene sequences from major eukaryotic lineages using maximum likelihood, minimum evolution, and maximum parsimony supported Ancyromonas forming its own lineage, called Ancyromonadida, that is more closely related to opisthokonts than its nearest protist relatives. However, low bootstrap support for deep nodes limits the ability of 18S rDNA to fully resolve this aspect of eukaryotic phylogeny.
The document reports on a study that identified quantitative trait loci (QTLs) associated with stigma exertion rate and spikelet number per panicle in rice. Eight QTLs for single stigma exertion, double stigma exertion, and total stigma exertion were detected on chromosomes 6, 10, 11 and three QTLs for spikelet number per panicle were identified on chromosomes 1 and 3. One QTL for spikelet number was detected in two different environments. The study provides information to aid in fine mapping, gene cloning and marker-assisted selection for improving hybrid rice seed production.
This study investigates the population of bluntnose sixgill sharks (Hexanchus griseus) in the Central Mediterranean Sea, particularly around the Maltese Islands. Over 435 sharks were sampled between 2004-2008 from a fish market in Malta. Samples were collected and recorded for weight, length, sex, and location. Genetic analysis of tissue samples is being conducted to study population structure using mtDNA and microsatellites. Preliminary results show sizes of sampled sharks, with no gravid females found. The aim is to use genetic and morphological data to understand the species' regional status and inform fishery management.
Genomic gene expression changes resulting from Trypanosomiasis: a horizontal study Examining expression changes elucidated by micro arrays in seminal tissues associated with the pathophysiology of Trypanosomiasis during disease progression
Molecular characterization of rice (Oryza sativa L.) genotypes using target r...Innspub Net
In the present investigation, based on the seven rice putative candidate iron transporter genes, novel TRAP markers were developed. These markers were successfully employed in the molecular diversity study among 30 rice genotypes representing improved rice cultivars and land races with varied grain iron content (7.38 - 30.58 ppm). Totally, thirty TRAP primer combinations were screened, which generated 703 bands out of which 654 were polymorphic (93%) with an average of 21.8 bands per primer combination. The average polymorphic information content (PIC) values ranged from 0.09 (Osysl4b+ME05) to 0.25 (Osnramp5c+ME05, Osnramp1b+ME02 and Osysl4a +ME02). Gene diversity (H ˆ
) ranged from 0.10 (Osysl4b+ME05) to 0.31 (Osnramp1b + ME02 and Osysl4a +ME02). The Jaccard dissimilarity ranged from 0.15 to 0.52, explaining 37% of genetic variation (Table 4). Grouping of genotypes based on UPGMA and principal coordinate analysis (PCoA) were found comparable and grouping of genotypes into a different cluster was found mainly on the basis of pedigree relationships. TRAP markers revealed well resolved relationships among rice genotypes. The information generated from this study will helps to select parental combinations for breeding high iron content
rice varieties.
1) The study investigated the effects of the tyrosine kinase inhibitors crizotinib and dasatinib on canine osteosarcoma cell lines. It found that dasatinib more effectively suppressed cell viability and inhibited hepatocyte growth factor-induced invasion and migration compared to crizotinib.
2) Exogenous hepatocyte growth factor increased invasion, migration, and matrix metalloproteinase production in the osteosarcoma cell lines.
3) Preliminary results showed that four dogs with osteosarcoma treated with adjuvant dasatinib therapy experienced an apparent clinical benefit.
The Effects of Genetic Alteration on Reprogramming of Fibroblasts into Induc...remedypublications2
Induced Pluripotent Stem Cells (iPSCs) can be generated from somatic cells by ectopic expression of
Yamanaka factors (
Oct4
,
Sox2
,
Klf4
and
c-Myc
) or combination of other factors. Genetic alteration
of fibroblasts exhibits an effect on reprogramming efficiency through multiple signaling pathways,
including epigenetic modifications, metabolic shifts, Mesenchymal-To-Epithelial Transition
(MET) and cell proliferation. In order to better understand the underlying mechanisms in cell fate
determination, in this review we will summarize several genetic alterations involved in the regulation
of reprogramming fibroblasts into iPSCs.
This document summarizes the mapping of genetic sequences disclosed in patents onto the maize, rice, soybean, and human genomes. The key findings are:
- 2.8 million patent sequences were mapped to each of the maize and soybean genomes, and 2.5 million to the rice genome, compared to 31 million mapped to the human genome.
- Less than 0.3% of mapped sequences for plant genomes were referenced in patent claims, compared to over 1% for the human genome.
- Over 80% of sequences mapped to plant genomes overlapped with sequences from other genomes, including the human genome. Only 12% of human sequences overlapped with plant genomes.
- 3,
Pells et al [2015] PLoS ONE 10[7] e0131102Steve Pells
This research article identifies novel human embryonic stem cell regulators based on their conserved and distinct CpG island methylation patterns. The researchers analyzed CpG island methylation in four human embryonic stem cell lines using a CpG island array and identified 1,111 CpGs that were methylated in all stem cell lines. They compared the methylation profiles to somatic tissues and mRNA expression data to identify stem cell-specific methylation patterns associated with gene expression. Genes related to transcriptional repression and activation were overrepresented among genes associated with methylated or unmethylated CpGs specifically in stem cells. Knockdown experiments confirmed that some candidate regulators induced stem cell differentiation, while overexpression modulated induced pluripotent stem cell formation
The document reviews protocols for generating induced pluripotent stem cells (iPSCs) including choice of reprogramming factors, delivery methods, and target cell types. The core reprogramming factors are Oct4, Sox2, Klf4, and c-Myc, though variations exist. Initial methods used integrating viruses but newer approaches aim to be non-integrating. Fibroblasts are commonly used as starting cells but iPSCs have been made from other cell types. Standardization of parameters can improve comparisons between experiments.
This document describes the development of a multiplex PCR assay targeting the cgcA gene, which encodes a diguanylate cyclase, to differentiate between species within the genus Cronobacter. Analysis of 12 Cronobacter genomes identified 7 conserved diguanylate cyclase-encoding genes, one of which, cgcA, showed species-specific divergence that matched known phylogenetic relationships between Cronobacter species. Primers were designed for this gene and tested in a multiplex PCR assay on 305 Cronobacter isolates representing 6 species. The assay correctly identified the species of all isolates tested and did not identify any of 20 non-Cronobacter species, demonstrating high specificity and sensitivity for rapid identification of Cronobacter.
This study assessed the effects of three centrifugal forces (600×g, 3000×g, and 6000×g for 10 minutes at room temperature) on ram sperm motility and functionality. Higher centrifugal forces resulted in greater sperm packaging but also had deleterious effects on sperm quality. Centrifugation at 3000×g and 6000×g impaired sperm movement patterns after 2 hours of incubation at 37°C compared to lower forces. While viability was not significantly different between groups, apoptotic sperm increased in the 6000×g samples immediately after centrifugation. The researchers concluded that centrifugal forces of 3000×g or greater induced harmful effects on ram sperm quality, and lower forces did not provide adequate sperm packaging.
CRISPR as a potential tool for malaria eradicationMatthias Samwald
Why avoiding delays to gene-drive based mosquito eradication should be the most important goal of the global community right now, and why it is not.
Presentation at the Vienna Rationality Meetup 14.05.2016
Este documento discute a necessidade de repensar a educação para promover o desenvolvimento sustentável em um mundo complexo. Defende uma abordagem humanista da educação que promova a inclusão, a justiça social e os direitos humanos. Também destaca a importância de considerar contextos locais e sistemas de conhecimento diversos ao formular políticas educacionais globais e locais.
Individual and demographic consequences of reduced body condition following r...João Soares
Repeated exposure to high temperatures (≥35°C) negatively impacted the body condition of White-plumed Honeyeaters, but only in dry conditions with low rainfall. Males with reduced body condition after heat exposure were less likely to be recaptured the following spring, suggesting higher mortality. Females and smaller individuals showed lower survival after heat exposure due to their smaller size. Over time, as maximum temperatures increased and rainfall declined, annual survival of the honeyeaters declined as well. Repeated exposure to heat stress may have contributed to increases in the average body size of the population by reducing survival of smaller birds.
The document outlines Trebuchet Financial Management Inc.'s methodology for achieving effective financial management in an organization. The methodology involves reviewing governance and accountability, establishing deliverables and forecasts for programs, creating a budget that supports overall organizational goals, collecting and understanding financial data, and reporting data in a timely and accurate manner to funders.
The document discusses a quantitative research study on the effectiveness of cranberry juice in treating urinary tract infections (UTIs) in women. A quantitative method was used to collect numerical data that could be analyzed statistically. The study involved an experimental group that received cranberry juice, a control group that received delayed or no treatment, and analysis of subgroup data through bivariate analysis. The implications were that understanding UTIs and finding natural treatment options like cranberry juice could help prevent suffering in women.
This document provides an overview of environmental change on Earth over time. It discusses how early humans began modifying their environment starting around 2 million years ago through activities like building shelters and controlling fire. It then describes major climate and environmental changes that occurred throughout history, including the impacts of glacial periods and the transition to agriculture around 10,000 years ago. The document outlines five major extinction events in Earth's history and how human activities have increasingly shaped the global environment as population has grown over the past 10,000 years.
The document summarizes key information about the Earth's atmosphere and major human impacts on it. It describes the atmosphere's composition and layers, and its vital roles in sustaining life through circulating gases and shielding the planet. It then discusses four major issues - ozone depletion caused by CFCs, global warming from increased greenhouse gases like carbon dioxide, the resulting climate change effects, and air pollution. The Antarctic ozone hole is described as the largest on record. Global warming is recognized as a serious threat and is mainly caused by human activities like fossil fuel use. Predicted consequences include rising sea levels and impacts on hundreds of millions of people.
Disc golf, also known as frisbee golf, involves throwing a frisbee or disc into a basket in as few throws as possible. Players need discs designed specifically for disc golf that come in different types for driving and putting. While disc golf courses provide a more professional setting, the game can also be played informally in parks, neighborhoods, or anywhere with a clear target. Disc golf is accessible for people of all skill levels as it combines exercise and fun. Losing discs in the woods is a common problem but also part of the challenge.
This document discusses human impacts on the environment that can now be objectively measured and seen from space. It summarizes a NASA study that used satellite imagery to create a map quantifying human influence across different regions of the world. The document also discusses several specific examples of human-caused environmental changes, such as declines in fish populations due to industrial fishing, increases in greenhouse gases affecting global climate, and the rapid growth of electronic waste. Satellite images taken over time are able to reveal human-induced changes to landscapes and ecosystems around the planet.
This document summarizes research on mitochondrial DNA (mtDNA) and its mutation rate. It discusses how mtDNA is inherited maternally and generally does not recombine. Two methods for estimating mtDNA mutation rates are pedigree analysis and phylogenetic analysis, which produce rates that differ by around 3 times. Both rates provide accurate estimates of divergence times depending on how closely or distantly sequences are related. The document also explores evidence of mtDNA recombination in one individual who inherited mitochondria from both parents.
This document discusses a new whole-genome based method for constructing phylogenetic trees of prokaryotes without sequence alignment. The method involves using the frequency distribution of k-tuples in complete proteomes to define compositional vectors for each species, and calculating distances between vectors to build trees. Tests recovered accepted relationships from rRNA trees and Bergey's Manual. The approach avoids issues with aligning whole genomes and is independent of genome size and gene content.
This document describes a study that analyzed the mitochondrial large subunit ribosomal RNA (LSU rRNA) sequences and secondary structures of 10 mollusk species. The researchers determined the complete nucleotide sequences and inferred the secondary structure models for each species. They found substantial length variation among taxa, with gastropods having the shortest lengths. Phylogenetic analysis supported monophyly of several taxa. Most notably, they discovered phylogenetic signal in the secondary structure of mollusk rRNA, with some gastropods uniquely lacking stem/loop structures, explaining much of the observed length variation.
This presentation contains basic information about the mouse being used as a model organism, its genome, how the genome of the mouse was sequenced and a comparison between mouse genome and human genome.
A Comparative Encyclopedia Of DNA Elements In The Mouse GenomeDaniel Wachtel
The Mouse ENCODE Consortium mapped transcription, chromatin accessibility, transcription factor binding, chromatin modifications, and replication domains in over 100 mouse cell types and tissues to generate a comparative encyclopedia of functional DNA elements in the mouse genome. They found that while much is conserved with humans, many mouse genes and large portions of regulatory DNA show divergence. Mouse and human transcription factor networks are more conserved than cis-regulatory DNA. Species-specific regulatory sequences are enriched for repetitive elements. Chromatin state and replication timing landscapes are developmentally stable within species.
Paper memo: Optimal-Transport Analysis of Single-Cell Gene Expression Identif...Ryohei Suzuki
This document summarizes a study that uses single-cell RNA sequencing data from mouse embryonic fibroblast cells undergoing reprogramming to induced pluripotent stem cells over 18 days. The study develops a new computational method called Waddington-optimal transport that models cell differentiation as an optimal transport problem to infer developmental trajectories and ancestor-descendant relationships between cells across time points. Applying this method to the reprogramming data revealed multiple cell fates including induced pluripotent stem cells, stromal cells, and trophoblast-like cells. It also identified transcription factors and signaling pathways important for reprogramming. The method provides a novel way to systematically analyze densely sampled temporal single-cell gene expression data.
This document summarizes a thesis that developed a database comparing gene expression data from axolotl and zebrafish limb regeneration studies. The thesis used a "Rosetta stone" approach to identify 78 axolotl genes that matched human genes and had homologous zebrafish genes. These genes were organized based on gene ontologies, functions during regeneration, and expression changes with TCDD exposure. Key findings included roles for ribosomal proteins, mitochondria, neurite regeneration, extracellular matrix proteins, and genes related to cell differentiation, apoptosis and maintenance.
This document presents a methodological pipeline to analyze the morphological diversity and evolution of marine tetrapods using multiple techniques:
1. Morphometric analyses of extinct and living marine tetrapods to numerically describe their diversity and derive a theoretical morphospace.
2. Computational fluid dynamic simulations to quantify functional parameters like lift, drag, and pressure around bodies under different conditions.
3. Phylogenetic comparative methods and morphospace analyses to test hypotheses about contingency vs. determinism in evolution by examining patterns of morphological convergence and disparity.
The goal is to gain insights into marine tetrapod evolution and the degree of determinism or flexibility in exploring morphological design space.
Feasibility of using 3D MR elastography to determine pancreatic stiffness in ...Nicole Freitag
This study evaluated the feasibility of using 3D MR elastography (MRE) to determine pancreatic stiffness in healthy volunteers. Twenty healthy volunteers underwent MRE exams of their pancreas at 40 Hz and 60 Hz vibration frequencies. The mean shear stiffness was calculated for different pancreatic subregions and the liver. Stiffness measurements were more consistent at 40 Hz vibration. This preliminary study suggests 3D MRE may provide reproducible pancreatic stiffness measurements and could help detect early pancreatic diseases in the future.
The document discusses the Human Genome Project, which had goals of identifying all 30,000 human genes, determining the sequence of the 3 billion base pairs that make up human DNA, storing this information in databases, and improving data analysis tools. By sequencing factories generating 1000 nucleotides per second, the project was completed ahead of schedule. The project revealed that humans have fewer genes than expected, 99.9% of bases are identical between humans, and 50% or more of the genome consists of "junk DNA" with unknown functions.
Dealing with heterogeneous data to improve our knowledge of biodiversity dynamics and ecosystem function: perspectives from synthesis projects: presented by Liliana Ballesteros-Meija for ACTIAS (Global patterns of insect diversity, distribution and evolutionary distinctness - What can we learn from two of the best-documented families of moths?) at the sfécologie conference 2018.
more information on the group: http://www.cesab.org/index.php/fr/projets-en-cours/projets-2014/130-actias
Effects of density on spacing patterns and habitat associations of a Neotropi...Nicole Angeli
Presentation at Ecological Society of America, August 2013. Minneapolis, USA. –Oral Paper
Angeli, N. F., K. Lips, G. V. DiRenzo, and A. Cunha. “Effects of density on spacing patterns
and habitat associations in the Neotropical Glassfrog Espadarana prosoblepon.”
Achilles is a circadian clock controlled gene that regulates immune function ...Edith Csiki-Fejér
This document summarizes research identifying a novel clock-controlled gene in Drosophila melanogaster called Achilles (Achl) that regulates the fly's immune system. The researchers found that Achl is rhythmically expressed at the mRNA level in the fly brain and acts to repress expression of antimicrobial peptides (AMPs) in the immune system. Knocking down Achl expression in fly neurons dramatically increased expression of immune response genes and made the flies more resistant to bacterial infection. However, this also reduced the flies' lifespans, indicating a cost to constantly activating the immune pathway. The findings demonstrate that Achl is a circadian clock-regulated gene that helps control the immune response in flies.
Los modelos teóricos presentados en este artículo pretenden mostrar porqué el exponente de ¾ de la ley de Kleiber puede surgir de las restricciones que impone distribuir los recursos a través de redes de ramificación jerárquica
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
Extracellular RNA (ex RNA) exists in nanoparticles called exosomes in human bodies. The document suggests that ex RNA is generated in the meridian, which is a proposed third circulatory system in addition to the blood and lymph systems. The author proposes identifying the meridian first using a specific dye, and then identifying and confirming ex RNA within it to understand the source of exosomes and ex RNA in the body.
Fernando de la Cruz presented a document on plasmid conjugation systems and controlling the dissemination of antibiotic resistance. The document contained the following key points:
1. The only element common among all conjugatively transmissible plasmids is the relaxase protein. Conjugative plasmids also contain VirB4 proteins.
2. Different types of plasmids - conjugative, mobilizable, and non-transmissible - were analyzed based on size. IncF and IncI plasmids frequently transfer antibiotic resistance.
3. COINs (conjugation inhibitory compounds) show potential to control the dissemination of multidrug resistance by inhibiting bacterial conjugation without affecting growth.
AAPA Poster. Insights from developmental genetics and reproductive isolation ...Craig Knox
The document analyzes mechanisms of reproductive isolation in hominin species to determine the number of biological species represented in the human fossil record. It finds that chromosomal isolation, specifically changes to the Hoxd gene sequence on chromosome 2, best explains speciation events. Analysis of vertebrae phenotypes in fossils, regulated by Hoxd genes, suggests fewer hominin species existed than typically recognized, supporting models of 5 or fewer biological species. The hypothesis that changes to Hoxd gene regulation caused transitions like the origin of bipedality can be empirically tested through molecular evolution methods.
Similar to 10 rapid molecular evolution in a living fossil (20)
A Abolicao do Trabalho-por Bob Black.pdfJoão Soares
No artigo intitulado “The Original Affluent Society” (Idade da Pedra, Sociedade da Abundância), o antropólogo Marshall Sahlins ao estudar os colectores de caça fez explodir o mito Hobbesiano. Os colectores de caça trabalham muito menos do que nós. Além disso, é difícil distinguir esse trabalho daquilo que nós consideramos hoje como divertimento. Sahlins diz que o “trabalho” dos caçadores e colectores em busca de alimento é intermitente e melhor do que o trabalho permanente. O descanso é abundante. Ao contrário da maioria de nós, dormem durante o dia. O trabalho que fazem — trabalham uma média de 4 horas por dia e supondo que aquilo que fazem é aos nossos olhos trabalho —, são esforços que parecem ser efectuados com habilidade e que provocam a evolução da capacidade física e intelectual. O trabalho indiferenciado em grande escala, como disse Sahlins, é impossível. Este tipo de trabalho (como modernamente também se designa, não qualificado), só se tomou possível com a industrialização.
The Open Society and Its Enemies- K. PopperJoão Soares
Written in political exile in New Zealand during the Second World War and published in two volumes in 1945, The Open Society and its Enemies was hailed by Bertrand Russell as a 'vigorous and profound defence of democracy'. This legendary attack on the philosophies of Plato, Hegel and Marx prophesied the collapse of communism in Eastern Europe and exposed the fatal flaws of socially engineered political systems. It remains highly readable, erudite and lucid and as essential reading today as on publication in 1945. It is available here in a special centenary single-volume edition.
DANÇAR O ZEN: APRENDIZADO E POÉTICAS DE UM PROCESSOJoão Soares
O documento discute um processo criativo experimental que relaciona o zen budismo, danças brasileiras e técnicas teatrais. O processo é ilustrado pela coreografia "O Touro e o Vazio", que incorpora elementos dos ritos zen, da estética anime japonesa e danças nordestinas brasileiras. A coreografia explora como essas diferentes técnicas e aprendizados podem traduzir a história do corpo que dança em busca de um "acontecer poético".
How Google enables Big Oil’s greenwashing-Final ReportJoão Soares
For the first time, the Center for Countering Digital Hate comprehensively details how Google enables Big Oil’s greenwashing. We reveal that nearly half of the $23.7 million spent on Google search ads by oil and gas companies in the last two years have targeted search terms on environmental sustainability. The five companies studied in this report, ExxonMobil, British Petroleum (BP), Chevron, Shell, and Aramco, have polluted our search results while Google raked in their dirty money.
The Entropy Law and the Economic ProcessJoão Soares
"Every few generations a great seminal book comes along that challenges economic analysis and through its findings alters men's thinking and the course of societal change. This is such a book, yet it is more. It is a "poetic" philosophy, mathematics, and science of economics. It is the quintessence of the thought that has been focused on the economic reality. Henceforce all economists must take these conclusions into account lest their analyses and scholarship be found wanting. "The entropy of the physical universe increases constantly because there is a continuous and irrevocable qualitative degradation of order into chaos. The entropic nature of the economic process, which degrades natural resources and pollutes the environment, constitutes the present danger. The earth is entropically winding down naturally, and economic advance is accelerating the process. Man must learn to ration the meager resources he has so profligately squandered if he is to survive in the long run when the entropic degradation of the sun will be the crucial factor, "for suprising as it may seem, the entire stock of natural resources is not worth more than a few days of sunlight!" Georgescu-Rogen has written our generation's classic in the field of economics."— Library Journal
E-Livro - Elogio da Loucura, por Erasmo de RoterdãoJoão Soares
Esta célebre é incontornável obra, ainda que com mais de 500 anos, continua atual. O autor levanta o véu que cobre e tolda o olhar e humano, numa denúncia dos comportamentos sociais. É introduzida a linha do Humanismo nesta amálgama satírica.
Constituição da República Portuguesa 1976João Soares
O documento apresenta a Constituição da República Portuguesa, aprovada em 1976 após a Revolução dos Cravos. Ela estabelece Portugal como uma república democrática e socialista, comprometida com a independência nacional, os direitos humanos e a transição para o socialismo. A Constituição também define os princípios fundamentais do Estado, como a soberania popular e o Estado de Direito, assim como os direitos e deveres dos cidadãos portugueses.
War is a crime against humanity: The Story of War Resisters’ InternationalJoão Soares
This document provides a summary of the book "War is a Crime Against Humanity: The Story of War Resisters' International" by Devi Prasad. It details the history and work of the War Resisters' International organization from its founding in the 1920s through 1975. The document contains 13 chapters that describe the growth of pacifism and nonviolent movements throughout history, the founding and early work of WRI opposing World War I and conscription, and WRI's efforts to support war resisters and promote peace during and after World War II and through various 20th century conflicts. It also includes appendices with details on WRI conferences, leadership, publications, and affiliates around the world.
Extending Russia: Competing from Advantageous GroundJoão Soares
This report examines a range of possible means to extend Russia. As the 2018 National Defense Strategy recognized, the United States is currently locked in a great-power competition with Russia. This report seeks to define areas where the United States can compete to its own advantage. Drawing on quantitative and qualitative data from Western and Russian sources, this report examines Russia's economic, political, and military vulnerabilities and anxieties. It then analyzes potential policy options to exploit them — ideologically, economically, geopolitically, and militarily (including air and space, maritime, land, and multidomain options). After describing each measure, this report assesses the associated benefits, costs, and risks, as well as the likelihood that measure could be successfully implemented and actually extend Russia. Most of the steps covered in this report are in some sense escalatory, and most would likely prompt some Russian counter-escalation. Some of these policies, however, also might prompt adverse reactions from other U.S. adversaries — most notably, China — that could, in turn, stress the United States. Ultimately, this report concludes that the most attractive U.S. policy options to extend Russia — with the greatest benefits, highest likelihood of success, and least risk — are in the economic domain, featuring a combination of boosting U.S. energy production and sanctions, providing the latter are multilateral. In contrast, geopolitical measures to bait Russia into overextending itself and ideological measures to undermine the regime's stability carry significant risks. Finally, many military options — including force posture changes and development of new capabilities — could enhance U.S. deterrence and reassure U.S. allies, but only a few are likely to extend Russia, as Moscow is not seeking parity with the United States in most domains.
Pensar Portugal – A modernidade de um país antigoJoão Soares
Pensar Portugal – A Modernidade de um País Antigo é um livro de pequenos ensaios de ciências sociais e humanas, que apresentam e discutem assuntos e problemas relativos a Portugal. São ensaios que constituem estudos de caso, embora tenham a forma de crónicas. O ponto de vista não é propriamente filosófico, nem estético, nem político. É um exercício de compreensão do mundo contemporâneo, tendo as ciências sociais e humanas como enquadramento teórico. Estes ensaios filiam-se no reconhecimento de um pensamento da prática, e também no reconhecimento da importância do imaginário em toda a estruturação social. O livro está organizado em seis partes. Cada parte é iniciada por um capítulo teórico. A função destes capítulos é a de enquadrar, teórica e metodologicamente, os pequenos ensaios, colocadas no registo específico de cada uma das partes do livro.
Bulletin of the Atomic Scientisits 2024-Doomsday-Clock-StatementJoão Soares
The document summarizes the 2024 Doomsday Clock statement from the Bulletin of the Atomic Scientists. It finds that humanity faces an unprecedented level of danger from nuclear weapons, climate change, disruptive technologies, and other threats. The Doomsday Clock remains set at 90 seconds to midnight, the closest it has ever been to catastrophe. Key threats include an increased risk of nuclear war due to conflicts like Ukraine, an accelerating climate crisis, and dangers from emerging technologies like AI and biotechnology if left unchecked. Urgent global cooperation is needed to reduce threats and move the clock further from midnight.
The Man in The High Castle Philip K. DickJoão Soares
This document provides bibliographic and copyright information for the novel "The Man in the High Castle" by Philip K. Dick. It includes a dedication to the author's wife, acknowledgments for sources used, and the beginning of Chapter 1 which introduces the main character Mr. Robert Childan and describes his antique store in San Francisco.
o homem do castelo alto - philip k. dickJoão Soares
1) O documento apresenta uma introdução a uma nova edição do livro "O Homem do Castelo Alto" de Philip K. Dick, traduzido para português.
2) O autor revisita um texto introdutório que escreveu há 27 anos sobre a obra e pensamento de Philip K. Dick.
3) A introdução discute a vida e carreira de Philip K. Dick, sua visão do mundo, influências filosóficas e religiosas, e como isso é refletido em sua ficção científica.
Falsas catástrofes invisíveis e ameaças de destruiçãoJoão Soares
This document summarizes and critiques a news article claiming that Africa's oldest baobab trees are dying at an unprecedented rate that may be caused by climate change. The summary critiques several aspects of the original claim:
1) It is normal for older trees and species to die, yet the article provides no baseline rate of baobab mortality to say if the current rate is truly unprecedented.
2) The article only speculates that climate change "may" be the cause, providing no actual evidence of a link between climate change and baobab deaths.
3) There are no population figures for baobabs across Africa to determine mortality rates, yet the article claims the rate of death is increasing
Introdução ao pensamento feminista negroJoão Soares
O texto defende um feminismo que abarque as 99% das mulheres, especialmente as mais vulneráveis e marginalizadas, como mulheres negras, pobres, indígenas, trabalhadoras domésticas e LGBTQIA+. O feminismo proposto é anticapitalista, antirracista, ecossocialista e contra a opressão de gênero, classe e raça.
Queer Palestine and the Empire of CritiqueJoão Soares
This document provides background on the author's personal experiences coming to terms with his queer identity as a Palestinian. He describes growing up feeling different from his peers and hearing anti-gay messages. During college, he began exploring queer identities but still felt isolated due to differences in experiences. Exposure to queer communities in the US and Middle East helped his acceptance. The author's academic work has focused on critiquing universalizing of Western LGBT concepts and embracing a nuanced understanding of queer identities and experiences of Arabs. His journey highlights tensions between queer and Arab identities but also their connections within himself.
Removing Uninteresting Bytes in Software FuzzingAftab Hussain
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
In his public lecture, Christian Timmerer provides insights into the fascinating history of video streaming, starting from its humble beginnings before YouTube to the groundbreaking technologies that now dominate platforms like Netflix and ORF ON. Timmerer also presents provocative contributions of his own that have significantly influenced the industry. He concludes by looking at future challenges and invites the audience to join in a discussion.
OpenID AuthZEN Interop Read Out - AuthorizationDavid Brossard
During Identiverse 2024 and EIC 2024, members of the OpenID AuthZEN WG got together and demoed their authorization endpoints conforming to the AuthZEN API
Cosa hanno in comune un mattoncino Lego e la backdoor XZ?Speck&Tech
ABSTRACT: A prima vista, un mattoncino Lego e la backdoor XZ potrebbero avere in comune il fatto di essere entrambi blocchi di costruzione, o dipendenze di progetti creativi e software. La realtà è che un mattoncino Lego e il caso della backdoor XZ hanno molto di più di tutto ciò in comune.
Partecipate alla presentazione per immergervi in una storia di interoperabilità, standard e formati aperti, per poi discutere del ruolo importante che i contributori hanno in una comunità open source sostenibile.
BIO: Sostenitrice del software libero e dei formati standard e aperti. È stata un membro attivo dei progetti Fedora e openSUSE e ha co-fondato l'Associazione LibreItalia dove è stata coinvolta in diversi eventi, migrazioni e formazione relativi a LibreOffice. In precedenza ha lavorato a migrazioni e corsi di formazione su LibreOffice per diverse amministrazioni pubbliche e privati. Da gennaio 2020 lavora in SUSE come Software Release Engineer per Uyuni e SUSE Manager e quando non segue la sua passione per i computer e per Geeko coltiva la sua curiosità per l'astronomia (da cui deriva il suo nickname deneb_alpha).
Essentials of Automations: The Art of Triggers and Actions in FMESafe Software
In this second installment of our Essentials of Automations webinar series, we’ll explore the landscape of triggers and actions, guiding you through the nuances of authoring and adapting workspaces for seamless automations. Gain an understanding of the full spectrum of triggers and actions available in FME, empowering you to enhance your workspaces for efficient automation.
We’ll kick things off by showcasing the most commonly used event-based triggers, introducing you to various automation workflows like manual triggers, schedules, directory watchers, and more. Plus, see how these elements play out in real scenarios.
Whether you’re tweaking your current setup or building from the ground up, this session will arm you with the tools and insights needed to transform your FME usage into a powerhouse of productivity. Join us to discover effective strategies that simplify complex processes, enhancing your productivity and transforming your data management practices with FME. Let’s turn complexity into clarity and make your workspaces work wonders!
Generating privacy-protected synthetic data using Secludy and MilvusZilliz
During this demo, the founders of Secludy will demonstrate how their system utilizes Milvus to store and manipulate embeddings for generating privacy-protected synthetic data. Their approach not only maintains the confidentiality of the original data but also enhances the utility and scalability of LLMs under privacy constraints. Attendees, including machine learning engineers, data scientists, and data managers, will witness first-hand how Secludy's integration with Milvus empowers organizations to harness the power of LLMs securely and efficiently.
Monitoring and Managing Anomaly Detection on OpenShift.pdfTosin Akinosho
Monitoring and Managing Anomaly Detection on OpenShift
Overview
Dive into the world of anomaly detection on edge devices with our comprehensive hands-on tutorial. This SlideShare presentation will guide you through the entire process, from data collection and model training to edge deployment and real-time monitoring. Perfect for those looking to implement robust anomaly detection systems on resource-constrained IoT/edge devices.
Key Topics Covered
1. Introduction to Anomaly Detection
- Understand the fundamentals of anomaly detection and its importance in identifying unusual behavior or failures in systems.
2. Understanding Edge (IoT)
- Learn about edge computing and IoT, and how they enable real-time data processing and decision-making at the source.
3. What is ArgoCD?
- Discover ArgoCD, a declarative, GitOps continuous delivery tool for Kubernetes, and its role in deploying applications on edge devices.
4. Deployment Using ArgoCD for Edge Devices
- Step-by-step guide on deploying anomaly detection models on edge devices using ArgoCD.
5. Introduction to Apache Kafka and S3
- Explore Apache Kafka for real-time data streaming and Amazon S3 for scalable storage solutions.
6. Viewing Kafka Messages in the Data Lake
- Learn how to view and analyze Kafka messages stored in a data lake for better insights.
7. What is Prometheus?
- Get to know Prometheus, an open-source monitoring and alerting toolkit, and its application in monitoring edge devices.
8. Monitoring Application Metrics with Prometheus
- Detailed instructions on setting up Prometheus to monitor the performance and health of your anomaly detection system.
9. What is Camel K?
- Introduction to Camel K, a lightweight integration framework built on Apache Camel, designed for Kubernetes.
10. Configuring Camel K Integrations for Data Pipelines
- Learn how to configure Camel K for seamless data pipeline integrations in your anomaly detection workflow.
11. What is a Jupyter Notebook?
- Overview of Jupyter Notebooks, an open-source web application for creating and sharing documents with live code, equations, visualizations, and narrative text.
12. Jupyter Notebooks with Code Examples
- Hands-on examples and code snippets in Jupyter Notebooks to help you implement and test anomaly detection models.
Things to Consider When Choosing a Website Developer for your Website | FODUUFODUU
Choosing the right website developer is crucial for your business. This article covers essential factors to consider, including experience, portfolio, technical skills, communication, pricing, reputation & reviews, cost and budget considerations and post-launch support. Make an informed decision to ensure your website meets your business goals.
Your One-Stop Shop for Python Success: Top 10 US Python Development Providersakankshawande
Simplify your search for a reliable Python development partner! This list presents the top 10 trusted US providers offering comprehensive Python development services, ensuring your project's success from conception to completion.
Ivanti’s Patch Tuesday breakdown goes beyond patching your applications and brings you the intelligence and guidance needed to prioritize where to focus your attention first. Catch early analysis on our Ivanti blog, then join industry expert Chris Goettl for the Patch Tuesday Webinar Event. There we’ll do a deep dive into each of the bulletins and give guidance on the risks associated with the newly-identified vulnerabilities.
Driving Business Innovation: Latest Generative AI Advancements & Success StorySafe Software
Are you ready to revolutionize how you handle data? Join us for a webinar where we’ll bring you up to speed with the latest advancements in Generative AI technology and discover how leveraging FME with tools from giants like Google Gemini, Amazon, and Microsoft OpenAI can supercharge your workflow efficiency.
During the hour, we’ll take you through:
Guest Speaker Segment with Hannah Barrington: Dive into the world of dynamic real estate marketing with Hannah, the Marketing Manager at Workspace Group. Hear firsthand how their team generates engaging descriptions for thousands of office units by integrating diverse data sources—from PDF floorplans to web pages—using FME transformers, like OpenAIVisionConnector and AnthropicVisionConnector. This use case will show you how GenAI can streamline content creation for marketing across the board.
Ollama Use Case: Learn how Scenario Specialist Dmitri Bagh has utilized Ollama within FME to input data, create custom models, and enhance security protocols. This segment will include demos to illustrate the full capabilities of FME in AI-driven processes.
Custom AI Models: Discover how to leverage FME to build personalized AI models using your data. Whether it’s populating a model with local data for added security or integrating public AI tools, find out how FME facilitates a versatile and secure approach to AI.
We’ll wrap up with a live Q&A session where you can engage with our experts on your specific use cases, and learn more about optimizing your data workflows with AI.
This webinar is ideal for professionals seeking to harness the power of AI within their data management systems while ensuring high levels of customization and security. Whether you're a novice or an expert, gain actionable insights and strategies to elevate your data processes. Join us to see how FME and AI can revolutionize how you work with data!
Building Production Ready Search Pipelines with Spark and MilvusZilliz
Spark is the widely used ETL tool for processing, indexing and ingesting data to serving stack for search. Milvus is the production-ready open-source vector database. In this talk we will show how to use Spark to process unstructured data to extract vector representations, and push the vectors to Milvus vector database for search serving.
In the rapidly evolving landscape of technologies, XML continues to play a vital role in structuring, storing, and transporting data across diverse systems. The recent advancements in artificial intelligence (AI) present new methodologies for enhancing XML development workflows, introducing efficiency, automation, and intelligent capabilities. This presentation will outline the scope and perspective of utilizing AI in XML development. The potential benefits and the possible pitfalls will be highlighted, providing a balanced view of the subject.
We will explore the capabilities of AI in understanding XML markup languages and autonomously creating structured XML content. Additionally, we will examine the capacity of AI to enrich plain text with appropriate XML markup. Practical examples and methodological guidelines will be provided to elucidate how AI can be effectively prompted to interpret and generate accurate XML markup.
Further emphasis will be placed on the role of AI in developing XSLT, or schemas such as XSD and Schematron. We will address the techniques and strategies adopted to create prompts for generating code, explaining code, or refactoring the code, and the results achieved.
The discussion will extend to how AI can be used to transform XML content. In particular, the focus will be on the use of AI XPath extension functions in XSLT, Schematron, Schematron Quick Fixes, or for XML content refactoring.
The presentation aims to deliver a comprehensive overview of AI usage in XML development, providing attendees with the necessary knowledge to make informed decisions. Whether you’re at the early stages of adopting AI or considering integrating it in advanced XML development, this presentation will cover all levels of expertise.
By highlighting the potential advantages and challenges of integrating AI with XML development tools and languages, the presentation seeks to inspire thoughtful conversation around the future of XML development. We’ll not only delve into the technical aspects of AI-powered XML development but also discuss practical implications and possible future directions.
1. 17 Biesecker, L.G. (2005) Mapping phenotypes to language: a proposal to
organize and standardize the clinical descriptions of malformations.
Clin. Genet. 68, 320–326
18 Loscalzo, J. et al. (2007) Human disease classification in the
postgenomic era: a complex systems approach to human
pathobiology. Mol. Syst. Biol. 3, 124
19 Oti, M. and Brunner, H.G. (2007) The modular nature of genetic
diseases. Clin. Genet. 71, 1–11
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network, with an application for prioritizing positional candidate
genes. Am. J. Hum. Genet. 78, 1011–1025
0168-9525/$ – see front matter ß 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tig.2007.12.005
Genome Analysis
Rapid molecular evolution in a living fossil
Jennifer M. Hay1
, Sankar Subramanian1
, Craig D. Millar2
, Elmira Mohandesan1
and
David M. Lambert1
1
Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University,
Private Bag 102904 NSMC, Auckland, New Zealand
2
Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private 92019,
Auckland, New Zealand
The tuatara of New Zealand is a unique reptile that
coexisted with dinosaurs and has changed little morpho-
logically from its Cretaceous relatives. Tuatara have very
slow metabolic and growth rates, long generation times
and slow rates of reproduction. This suggests that the
species is likely to exhibit a very slow rate of molecular
evolution. Our analysis of ancient and modern tuatara
DNA shows that, surprisingly, tuatara have the highest
rate of molecular change recorded in vertebrates. Our
work also suggests that rates of neutral molecular and
phenotypic evolution are decoupled.
The uniqueness of tuatara
The tuatara (Sphenodon punctatus), found only in New
Zealand, is the last surviving member of a distinct reptilian
order Sphenodontia that lived alongside early dinosaurs
and separated from other reptiles in the Upper Triassic
>220 million years ago [1,2]. The skeletal morphology of
modern tuatara shows a remarkable similarity to some
Cretaceous sphenodontian fossils [1], which has led to
them being described as a ’living fossil’ [2]. In addition
to their stable morphology, tuatara are characterized by
several distinct physiologic features that are uncommon
among reptiles. They have low body temperatures (they
are active down to 5 8C in the wild); slow rates of growth
($50 cm in 35 years); a slow metabolism; a long generation
time (sexual maturity at 10–15 years) and a slow repro-
ductive rate (at 2- to 5-year intervals) [3–5]. It has been
argued that generation time, metabolic rate, body
temperature and body size [6,7] modulate the rate of
neutral molecular evolution. In tuatara, the rare combi-
nation of slow rates of morphological evolution, growth and
metabolism suggest that rates of neutral DNA sequence
evolution should be slow. To examine this, we sequenced
the mitochondrial DNA hypervariable regions (HVRs) of
the control region from the modern and known-age ancient
tuatara individuals and estimated the rate of evolution of
this region.
Estimation of molecular evolutionary rate using ancient
DNA methodology
Traditionally rates of molecular evolution have been esti-
mated using phylogenetic methods, in which levels of
genetic divergence among closely related species have been
calibrated against time points in the fossil record. How-
ever, this is not possible in tuatara because there are no
closely related species, one of the characteristics of ‘living
fossils’. Instead, we recovered nucleotide sequences from
known-age sub-fossil bones of tuatara, and using Bayesian
statistics, we estimated the rate of molecular evolution of
the mitochondrial hypervariable regions.
We amplified and sequenced mitochondrial DNA
(mtDNA) sequences from sub-fossil bones of 33 ancient
tuatara and from blood samples of 41 modern individuals
covering the range of modern populations and ancient sites
(for locations of modern and ancient samples and methods,
see online supplementary material). We had 29 bones
radiocarbon dated and inferred dates of four more from
a well-stratified site; the ages of the bones range from 650
to 8750 years BP. A 468-bp DNA sequence (including align-
ment gaps) from the mitochondrial control region (HVR I
and HVR II) was recovered in three nonoverlapping frag-
ments from the ancient samples, and a 1039-bp sequence
covering the control region and flanking tRNAs from the
modern populations, but we used just the 468 bp
sequenced in the ancient samples in these analyses (Gen-
Bank accession numbers EU394280-EU394353). We used
Bayesian statistics based on a Markov chain Monte Carlo
(MCMC) approach to estimate the evolutionary rate of the
HVR sequences (online supplementary material). The rate
estimate was obtained using a general time-reversible
model of evolution. To account for the rate variation among
nucleotide positions, we used a discrete gamma distri-
bution of six rate categories. The rate was estimated
assuming a constant population size and a relaxed uncor-
related log-normal molecular clock.Corresponding author: Lambert, D.M. (D.M.Lambert@massey.ac.nz).
Update Trends in Genetics Vol.24 No.3
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2. Higher rate of molecular evolution in tuatara
Our analysis shows that the mitochondrial HVR regions of
tuatara evolve at a rate of 1.56 [highest probability density
(HPD) 0.83–2.34] substitutions per nucleotide per million
years. This estimate remained almost the same when
modifying a range of prior assumptions such as substi-
tution model, molecular clock and population growth
(online supplementary material). In additional analyses,
Figure 1. Comparison of evolutionary rates of the mitochondrial hypervariable regions (HVR) regions of tuatara with rates estimated from nine other vertebrate species. The
evolutionary rate was estimated using 33 ancient and 41 modern sequences of tuatara. We used Bayesian statistics based on a Markov chain Monte Carlo (MCMC) approach
that accounts for various evolutionary parameters such as base composition, population size, rate and model of evolution using the software BEAST [24]. To model the
pattern of nucleotide evolution, sophisticated models such as Hasegawa-Kishino-Yano (HKY) and General Time-Reversible (GTR) were used. To account for the variation in
the rate of evolution among nucleotide positions, a discrete gamma distribution of six rate categories was used. Wide uniform prior distributions were used to avoid any
bias caused by restricted prior assumptions. For the estimation of the evolutionary rate in tuatara, priors were set to range from 10À10
to 1 substitution per site per year, and
in the case of population size, from 107
to 1 individuals. Both strict and relaxed molecular clock models were used for rate estimation and for each model constant and
exponential population growth assumptions were examined. The rate estimates were sampled once per 1000 cycles from the total MCMC chain length of 10 000 000 after
discarding the initial burn-in 1,000 000 steps. The posterior distributions were examined using the software TRACER [25], and the effective sample sizes (ESSs) for mean
evolutionary rate, population size and posterior likelihood were found to be >100 for all the models used. Our analysis showed that the rate of molecular evolution in
tuatara HVR regions is 1.56 [highest posterior density (HPD) intervals (0.83–2.34)] substitutions per nucleotide per million years. Although this result is based on relaxed
molecular clock and constant population size assumptions, the rate estimate and highest HPD (yellow area) were similar when varying several a priori assumptions (see
Supplementary Table S5). The evolutionary rate estimates for nine other vertebrates were obtained from previously published studies that used ancient DNA methods and
Bayesian MCMC statistics similar to this study [10,16,26–29]. The rate estimates obtained for ox, horse, moa and cave lion were adjusted for ancient DNA damage. However,
this does not bias our result (see main text). The Latin name, the length of the HVRs (bp), sample size and the age of the samples (thousand years) are as follows: Tuatara
(Sphenodon punctatus, 460; 76; 0–9), Ade´lie penguin (Pygoscelis adeliae; 313; 96; 0–7), aurochs (Bos primigenius, 379; 40; 2–12), Mappin’s moa (Pachyornis mappini; 241;
14; 1–6), bison (Bison bison/Bison priscus; 601; 182; 0–60), brown bear (Ursus arctos; 130; 30; 10–59), cave bear (Ursus spelaeus; 288; 26; 27–80), cave lion (Panthera leo
spelaea; 213; 34; 12–62), ox (Bos taurus; 379; 36; 4–6) and horse (Equus caballus; 348; 12; 1–28). Error bars indicate the HPD intervals.
Update Trends in Genetics Vol.24 No.3
107
3. we also used only the nucleotides present in all the ancient
and modern sequences (complete site deletion), and we
excluded the first four nucleotides that contain two dis-
tinct motifs (see online supplementary material). This
produced a conservative rate estimate of 1.37 (HPD
0.66–2.2). Generally, evolutionary rates obtained using
traditional calibration methods estimate HVR rates at
$0.2 substitutions/bp/million years (MY) [8,9]. This esti-
mate is almost an order of magnitude lower than those
estimated using ancient DNA methods [10,11]. Because
the rates estimated by calibration are consistently lower
than those estimated from ancient DNA, we compared our
result only with previous studies (Figure 1) using the
latter approach. The rate estimates in Figure 1 show that
the evolutionary rate of the tuatara HVR regions is the
highest among the vertebrate species studied to date. This
rate is >50% faster than that of other vertebrates (Figure
1). Postmortem ancient DNA damage can cause nucleotide
changes that increase the estimate of the rate of molecular
evolution [12–15], as could sequencing ancient DNA
Numts instead of mtDNA. However, neither can be
invoked to explain the high rate of evolution in tuatara
because of the observed similarities in ancient and mod-
ern HVR sequence (e.g. in nucleotide composition and
nucleotide pair frequencies; online supplementary
material). Recent studies have shown that the vast
majority of the ancient DNA damage results in C ! T
changes [16,17]. To examine this, we identified the orien-
tation of all the nucleotide changes in ancient and modern
HVR sequences using a maximum likelihood approach
implemented in the software PAML [18]. We found that
the ratio of C ! T to T ! C changes in the modern and
ancient populations were almost identical (2.71 and 2.66,
respectively, see Supplementary Table S4). Furthermore,
the sites of nucleotide substitution are the same in ancient
and modern samples (Supplementary Figure S3). There
are seven sites where there is variation only in multiple
ancient and no modern samples, but in each case the
individuals are in the same geographic location,
suggesting geographic variation rather than miscoding
lesions or Numts. A corroborating factor is that, in phy-
logenetic tree analyses (data not shown), branch lengths
to ancient samples are not consistently longer than to
modern samples. Ancient samples are from locations both
further north (warmer climate) and south (cooler) of mod-
ern populations, but there are no apparent north to south
or any other geographic or climatic cline in mutation
patterns to indicate environmentally selected variation
rather than neutral evolutionary change. These factors
further confirm that there was minimal postmortem
damage to the DNA, that the ancient sequences obtained
are authentic and that the unexpectedly high tuatara
evolutionary rates are real.
Neutral evolution and life history traits of tuatara
Given this high rate of molecular evolution, the stable
morphology of tuatara over tens of millions of years is
remarkable. By contrast, the birds and mammals shown
here (Figure 1) have undergone considerable morphologi-
cal change over the same period. The higher rate of tuatara
HVR evolution does not seem to be the result of a lineage-
specific effect, because the rate of evolution in other rep-
tiles is not higher than those recorded in birds and mam-
mals [19]. The observed higher rate of tuatara HVR
evolution does not support the hypothesized inverse
relationship between generation time and evolutionary
rates [20], because tuatara have a much longer generation
time (10–15 years) than do these birds and mammals
(<6 years). Our results also contradict the notion that
poikilothermic (cold-blooded) animals, such as tuatara,
should have slower rates of neutral molecular evolution
than homeothermic (warm-blooded) animals, such as
mammals and birds [6]. Other life history traits such as
body mass and metabolic rate cannot explain the elevated
rate of evolution in tuatara. The slow metabolic rate of
tuatara compared with other vertebrates suggests that the
reported positive relationship between metabolic rate and
molecular evolutionary rate cannot be generalized [6,7].
Furthermore, the rate of HVR evolution in tuatara is not
significantly different from the rates obtained for penguin,
aurochs or moa. This result argues against the effect of
body mass on the rate of nucleotide evolution [6,7], because
the body masses of the vertebrates shown in Figure 1 vary
up to three orders of magnitude (1–1000 kg).
Concluding remarks
Previous studies on living fossils such as the coelacanth
and the horseshoe crab have suggested a substantial
nucleotide diversity in these phylogenetically distinct
species [21,22], perhaps indirectly suggesting a high evol-
utionary rate. However, this is the first study to directly
estimate the rate of evolution in a living fossil and also the
first attempt to quantify the neutral evolutionary changes
in a species having such extreme physiologic and life
history traits. The results of our study support the hypoth-
esis that rates of neutral molecular and phenotypic evol-
ution are decoupled [23]. Hence, life history and
physiologic parameters do not explain all differences in
rates of neutral molecular evolution. Even if rates of
evolution are decoupled in nuclear and mitochondrial
DNA, metabolic rate theories [6,7] have suggested higher
temperatures may cause more oxidative damage in the
mitochondria and mtDNA. Perhaps the organization of the
mitochondrial genome, and the processes by which it tran-
scribes and replicates, might contribute more to our un-
derstanding of the diversity of rates of evolution across
major animal groups.
Acknowledgements
The authors thank the following for access to samples: modern, Charles
Daugherty and Stephen Sarre; ancient, Trevor Worthy, Alan Tennyson
(Museum of New Zealand), Neville Hudson (Geology Museum, University
of Auckland), Paul Scofield (Canterbury Museum), Karl Gillies, Lindsay
Hazley (Southland Museum) and Brian Gill (Auckland Museum). The
authors also thank Trevor Worthy for unpublished radiocarbon dates,
Judith Robins for independently verifying aDNA sequences, Leon
Huynen for help with cloning and the editor and four anonymous
reviewers for useful comments on the manuscript.
Supplementary data
Supplementary data associated with this article can
be found, in the online version, at doi:10.1016/j.tig.
2007.12.002.
Update Trends in Genetics Vol.24 No.3
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doi:10.1016/j.tig.2007.12.002 Available online 5 February 2008
Genome Analysis
Evolution of gene sequence and gene expression are
not correlated in yeast
Itay Tirosh1
and Naama Barkai2
1
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
2
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
We show that, in yeast, the divergence rate of gene
expression is not correlated with that of its associated
coding sequence. Gene essentiality influences both
modes of evolution, but other properties related to
protein structure or promoter composition are only cor-
related with coding-sequence divergence or gene expres-
siondivergence,respectively.Basedonthesefindings,we
discuss the possibilities of neutral evolution of gene
expression and of different modes of evolution in unicel-
lular versus multicellular organisms.
Two levels of gene’s evolutionary divergence
Phenotypic diversity is generated through changes in both
protein structure and protein regulation, but the connec-
tion between these two evolutionary modes is not well
understood. For example, neutral drift (lack of positive
selection) is known to have a major role in the evolution of
coding sequences, but the extent to which it contributes to
gene expression divergence is still under debate [1–3].
Furthermore, genetic properties that impact the rate of
evolution were derived for each mode independently but
were not compared systematically.
Previous attempts to examine the relationship between
the divergence of gene expression and that of the corre-
sponding coding sequences in multicellular organisms
gave conflicting results, with a positive correlation foundCorresponding author: Barkai, N. (naama.barkai@weizmann.ac.il).
Update Trends in Genetics Vol.24 No.3
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