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start [2017/09/08 18:05]
ramirez [Molecular Microbiology and Infection Unit]
start [2019/10/24 22:34] (current)
ramirez [The lab on the Web]
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 ====== Molecular Microbiology and Infection Unit ====== ====== Molecular Microbiology and Infection Unit ======
-{{:​ummi_bar.png|}} 
  
-/* {{:​hiring.jpeg?​direct&​200 |Hiring}} +{{:​hiring.jpeg?​direct&​200 |Hiring}} 
-Within the [[pip:​oneida_2017|ONEIDA]] project, we are looking for two **masters** with __**bioinformatics**__ skills. We are offering ​two [[https://imm.medicina.ulisboa.pt/pt/emprego/ofertas/immbi59-2017-e-immbi60-2017/|scolarships]] with a duration up to three yearsYou can also check these offers in the EraCareers portal ([[http://​www.eracareers.pt/​opportunities/​index.aspx?​task=showAnuncioOportunities&jobId=92336&​lang=en&​idc=1|Advertisement]]). */+Within the [[pip:​oneida_2017|ONEIDA]] project, we are looking for one **master** and two **PhD** with __**bioinformatics**__ skills. We are offering ​[[http://www.eracareers.pt/opportunities/index.aspx?​task=global&​jobId=119652|master fellowship]] and a [[http://www.eracareers.pt/opportunities/​index.aspx?​task=global&​jobId=119651|postdoctoral fellowship]] each with a duration ​of up to 14 monthsFor the other PhD we have opened a [[http://​www.eracareers.pt/​opportunities/​index.aspx?​task=global&jobId=119644|research contract]] with a duration of up to 14 months. 
 + 
 +We are looking for one **master** with expertise in __**clinical microbiology**__ or __**microbiology**__,​ including in the laboratory processing of samples for genomic sequencing for a [[http://​www.eracareers.pt/​opportunities/​index.aspx?​task=global&​jobId=119685|master fellowship]]
  
 The [[pip:​oneida_2017|ONEIDA]] project is a multidisciplinary inter-institutional project looking for the application of genomics in the context of infectious diseases and host-pathogen interactions. The [[pip:​oneida_2017|ONEIDA]] project is a multidisciplinary inter-institutional project looking for the application of genomics in the context of infectious diseases and host-pathogen interactions.
 +
 +Within the [[pip:​fct29676_2017|NGPHYLO]] project we are looking for one **master** with __**bioinformatics**__ skills. We are offering a [[http://​www.eracareers.pt/​opportunities/​index.aspx?​task=global&​jobId=119880|master fellowship]]
 +
 +/* Within the [[pip:​fct1555_2014|TransPneumo]] project, we are looking for one **bachelor** with __**bioinformatics**__ skills. We are offering a [[http://​www.eracareers.pt/​opportunities/​index.aspx?​task=global&​jobId=119685|bachelor fellowship]] with a duration of up to two years. /*
 +
 +/​*{{:​ummi_bar.png|}}*/​
 +
 +/* {{:​hiring.jpeg?​direct&​200 |Hiring}}
 +Within the [[pip:​oneida_2017|ONEIDA]] project, we are looking for two **masters** with __**bioinformatics**__ skills. We are offering two [[https://​imm.medicina.ulisboa.pt/​pt/​emprego/​ofertas/​immbi59-2017-e-immbi60-2017/​|scolarships]] with a duration up to three years. You can also check these offers in the EraCareers portal ([[http://​www.eracareers.pt/​opportunities/​index.aspx?​task=showAnuncioOportunities&​jobId=92336&​lang=en&​idc=1|Advertisement]]).
 +
 +The [[pip:​oneida_2017|ONEIDA]] project is a multidisciplinary inter-institutional project looking for the application of genomics in the context of infectious diseases and host-pathogen interactions. */
  
 /* {{:​hiring.jpeg?​direct&​200 |Hiring}} /* {{:​hiring.jpeg?​direct&​200 |Hiring}}
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 We are also looking for a **research fellow** to be involved in the __**clinical and molecular microbiology**__ work of [[pip|ONEIDA]] and we are offering a {{ ::​7-2017-bi-mramirez.pdf |fellowship}} with a duration up to three years. You can also check out this offer in the [[http://​www.eracareers.pt/​opportunities/​index.aspx?​task=global&​jobId=88418&​lang=pt|EraCareers portal]] or at [[https://​euraxess.ec.europa.eu/​site/​search?​keywords=IMM/​CT/​1-2017%20OR%20oneida|EURAXESS]]. */ We are also looking for a **research fellow** to be involved in the __**clinical and molecular microbiology**__ work of [[pip|ONEIDA]] and we are offering a {{ ::​7-2017-bi-mramirez.pdf |fellowship}} with a duration up to three years. You can also check out this offer in the [[http://​www.eracareers.pt/​opportunities/​index.aspx?​task=global&​jobId=88418&​lang=pt|EraCareers portal]] or at [[https://​euraxess.ec.europa.eu/​site/​search?​keywords=IMM/​CT/​1-2017%20OR%20oneida|EURAXESS]]. */
 ====== Description and Objectives ====== ====== Description and Objectives ======
-In spite of the successful use of antibiotics and vaccination,​ bacterial infections are still a major cause of morbidity and mortality worldwide. The changing demographics are shifting the attention to older adults where selective pressures may be radically different from those found in children. Several studies showed that bacterial populations are dominated by a few clones. The plasticity of bacterial genomes means that different isolates can carry a distinct array of antibiotic resistance and virulence genes. However, the relationship between carrying a certain gene complement and becoming a successful clone remains elusive. We have documented the bacterial population structure of several pathogens of the genus //​Streptococcus//​ and found differences between bacteria that are asymptomatically carried and those causing distinct infections in the various age groups. In addition, we identified genes that are unevenly distributed in the bacterial population, potentially explaining the propensity of certain clones for particular hosts or infections. We have also studied the flow of genetic information between bacteria and the factors enhancing or limiting these exchanges. In the future we plan to explore ​the differences between bacterial populations at the whole-genome level. We are refining existing approaches to handle ​next generation ​sequence data and are developing tools for storing and mining this data in a unified platform, integrating information from existing databases. We hope to get a detailed view of the genetic differences between bacterial clones and to identify candidate genes to explain their different abundance. We are also looking at streptococci causing infections in humans and animals to identify key events allowing the adaptation to different host species and to evaluate the current potential for zoonotic acquisition. Finally, we are determining the impact of the different pherotypes of //​Streptococcus pneumoniae//​ in creating conditions for genetic isolation within this species while also elucidating in detail the basis for the specific sensing of the two peptide pheromones. Understanding the dynamics and responses of a bacterial population to the multiple selective pressures imposed on it and the key genetic events allowing the differentiation of specific clones will allow us to better predict bacterial pathogen evolution. Our research also produces important epidemiological information ​that allow us to anticipate the potential benefits of vaccination or help guide the optimal empirical therapy for infections of suspected streptococcal etiology.+Despite ​the successful use of antibiotics and vaccination,​ bacterial infections are still a major cause of morbidity and mortality worldwide. The changing demographics are shifting the attention to older adults where selective pressures may be radically different from those found in children. Several studies showed that bacterial populations are dominated by a few clones. The plasticity of bacterial genomes means that different isolates can carry a distinct array of antibiotic resistance and virulence genes. However, the relationship between carrying a certain gene complement and becoming a successful clone remains elusive. We have documented the bacterial population structure of several pathogens of the genus //​Streptococcus//​ and found differences between bacteria that are asymptomatically carried and those causing distinct infections in the various age groups. In addition, we identified genes that are unevenly distributed in the bacterial population, potentially explaining the propensity of certain clones for particular hosts or infections. We have also studied the flow of genetic information between bacteria and the factors enhancing or limiting these exchanges ​and the role of mobile genetic elements in bacterial diversity. We are currently exploring ​the differences between bacterial populations at the whole-genome level. We are refining existing approaches to handle ​high throughput ​sequence ​(HTS) data and are developing tools for storing and mining this data in a unified platform, integrating information from existing databases. This is reflected in the development of novel bioinformatic tools with a focus on HTS. We hope to get a detailed view of the genetic differences between bacterial clones and to identify candidate genes to explain their different abundance. We are also looking at streptococci causing infections in humans and animals to identify key events allowing the adaptation to different host species and to evaluate the current potential for zoonotic acquisition. Understanding the dynamics and responses of a bacterial population to the multiple selective pressures imposed on it and the key genetic events allowing the differentiation of specific clones will allow us to better predict bacterial pathogen evolution. Our research also produces important epidemiological information ​allowing ​us to anticipate the potential benefits of vaccination or guiding ​the optimal empirical therapy for infections of suspected streptococcal etiology.
  
 ====== Research Areas ====== ====== Research Areas ======
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 ====== The lab on the Web ====== ====== The lab on the Web ======
  
-[[https://​imm.medicina.ulisboa.pt/​pt/investigacao/​laboratorios/​ramirez-lab/​|The lab on the IMM site]]\\+[[https://​imm.medicina.ulisboa.pt/​investigation/laboratories/mario-ramirez-lab/​#intro|The lab on the IMM site]]\\
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