List of the identified functions related to the differentially expressed tags. SuperSAGE tags fro... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags from the tolerant lentil genotypes considering both treatments – acclimation and control – together (XLSX 15 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags fro... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags from acclimated lentil plants considering both genotypes – susceptible and tolerant – together. (XLSX 15 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags fro... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags from non-acclimated lentil plants considering both genotypes – susceptible and tolerant – together. (XLSX 14 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags exc... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags exclusively observed in non- acclimated lentils of the frost-tolerant genotypes (NAT) and the corresponding sequences and gene functions identified. (XLSX 19 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags exc... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags exclusively observed in non-acclimated lentils of the frost-susceptible genotypes (NAS) and the corresponding sequences and gene functions identified. (XLSX 19 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags exc... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags exclusively observed in acclimated lentils of the frost-susceptible genotypes (AS) and the corresponding sequences and gene functions identified. (XLSX 18 kb)
Lists of significant Super-SAGE tags. Significant over represented SuperSAGE tags (fold change &g... more Lists of significant Super-SAGE tags. Significant over represented SuperSAGE tags (fold change >4) from the tolerant lentil RILs considering both treatments together (T). (XLSX 15 kb)
Differential response of some RILs to a treatment at −15 °C after 15 days of recovering. Note tha... more Differential response of some RILs to a treatment at −15 °C after 15 days of recovering. Note that while in most of the RILs all plantlets died, in one RIL the plantlets survived with little damage, and in some RILs a few plants survived but showing a lower growth. (JPEG 214 kb)
Additional list of functions. Summary of representative groups of related functions identified by... more Additional list of functions. Summary of representative groups of related functions identified by the different set of lentil tags. (XLSX 13 kb)
Overview of the heat stress conditions used in the study. (A) Pictograph showing the stress regim... more Overview of the heat stress conditions used in the study. (A) Pictograph showing the stress regime used for plant treatment as described in material and methods. (B) Representative photos of flower buds corresponding to different pollen stages. (C) Photos of pollen cells from different developmental stages, stained with the Alexander dye. Positive staining indicates viable pollen. (D) Bright field image of pollen at tetrad stage and fluorescent image of post-meiotic and mature pollen stained with DAPI, showing the single and double nuclei, respectively. (DOCX 2811 kb)
Novel putative miRNAs in post-meiotic pollen with their chromosomal position, mapping coordinates... more Novel putative miRNAs in post-meiotic pollen with their chromosomal position, mapping coordinates, sequence of the predicted miRNA precursor, star sequence, and mature sequence. (XLSX 71 kb)
Escherichia coli strain Nissle 1917 (EcN) is the active principle of a probiotic preparation (tra... more Escherichia coli strain Nissle 1917 (EcN) is the active principle of a probiotic preparation (trade name Mutaflor(®)) used for the treatment of patients with intestinal diseases such as ulcerative colitis and diarrhea. It has GRAS (generally recognized as save) status and has been shown to be a therapeutically effective drug (Sonnenborn and Schulze, 2009). The complete genomic DNA sequence will help in identifying genes and their products which are essential for the strains probiotic nature. Genbank/EMBL/DDBJ accession number: CP007799 (chromosome).
A 454-FLX low-coverage sequencing approach was used to assemble the mitochondrial genome of Radix... more A 454-FLX low-coverage sequencing approach was used to assemble the mitochondrial genome of Radix balthica. The mtDNA sequence is 13,993 nt long and contains 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs). Four genes, the 12S RNA and seven tRNAs are transcribed in reverse order. The sequence is AT rich (71.3%), similar to other basommatophoran species. Comparison with the most closely related mt genomes available (Biomphalaria glabrata and Biomphalaria tenagophila) revealed identical gene orders except for five tRNAs. Next generation sequencing proved to be a fast and easy method for sequencing an entire mitochondrial genome.
PurposeTo investigate the expression profile of the hypoxia-inducible transcription factor-1α (HI... more PurposeTo investigate the expression profile of the hypoxia-inducible transcription factor-1α (HIF-1α) and its downstream targets in malignancies of the ocular adnexa and to determine its relevance as a prognostic factor for clinical outcome.MethodsWe included 49 subjects with malignant tumours (25 squamous cell carcinomas (SCC), 15 non-Hodgkin lymphomas, 9 melanomas) and 30 patients with benign tumours of the ocular adnexa (13 papillomas, 7 reactive lymphoid hyperplasias (RLHs) and 10 nevi) as controls. We quantified HIF-1α protein expression by immunohistochemistry and assessed the association between HIF-1α and clinical outcome via Kaplan–Meier analysis. Furthermore, we assessed the expression of HIF-1α downstream factors by transcriptional sequencing using the MACE (massive analysis of cDNA ends) technology.ResultsSCCs revealed a strong HIF-1α expression in 61% of tumour cells in comparison with only 22% in papillomas (p < 0.0001). In contrast, malignant melanomas and lymphom...
Trabajo presentado en el IV International Ascochyta Workshop (Ascochyta 2016), celebrado en Troia... more Trabajo presentado en el IV International Ascochyta Workshop (Ascochyta 2016), celebrado en Troia (Portugal) el 10 y 11 de octubre de 2016.
The novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19... more The novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19 which has become a global concern due to its rapid spread. Meanwhile, increased demand in testing has led to shortage of reagents, supplies, and compromised the performance of diagnostic laboratories in many countries. Both the world health organization (WHO) and the Center for Disease Control and Prevention (CDC) recommend multi-step RT-PCR assays using multiple primer and probe pairs, which might complicate interpretation of the test results especially for borderline cases. In this study, we describe an alternative RT-PCR approach for the detection of SARS-CoV-2 RNA that can be used for the probe-based detection of clinical isolates in the diagnostics as well as in research labs using a low cost SYBR green method. For the evaluation, we used samples from patients with confirmed SARS-CoV-2 infection and performed RT-PCR assays along with successive dilutions of RNA standards to determi...
List of the identified functions related to the differentially expressed tags. SuperSAGE tags fro... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags from the tolerant lentil genotypes considering both treatments – acclimation and control – together (XLSX 15 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags fro... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags from acclimated lentil plants considering both genotypes – susceptible and tolerant – together. (XLSX 15 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags fro... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags from non-acclimated lentil plants considering both genotypes – susceptible and tolerant – together. (XLSX 14 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags exc... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags exclusively observed in non- acclimated lentils of the frost-tolerant genotypes (NAT) and the corresponding sequences and gene functions identified. (XLSX 19 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags exc... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags exclusively observed in non-acclimated lentils of the frost-susceptible genotypes (NAS) and the corresponding sequences and gene functions identified. (XLSX 19 kb)
List of the identified functions related to the differentially expressed tags. SuperSAGE tags exc... more List of the identified functions related to the differentially expressed tags. SuperSAGE tags exclusively observed in acclimated lentils of the frost-susceptible genotypes (AS) and the corresponding sequences and gene functions identified. (XLSX 18 kb)
Lists of significant Super-SAGE tags. Significant over represented SuperSAGE tags (fold change &g... more Lists of significant Super-SAGE tags. Significant over represented SuperSAGE tags (fold change >4) from the tolerant lentil RILs considering both treatments together (T). (XLSX 15 kb)
Differential response of some RILs to a treatment at −15 °C after 15 days of recovering. Note tha... more Differential response of some RILs to a treatment at −15 °C after 15 days of recovering. Note that while in most of the RILs all plantlets died, in one RIL the plantlets survived with little damage, and in some RILs a few plants survived but showing a lower growth. (JPEG 214 kb)
Additional list of functions. Summary of representative groups of related functions identified by... more Additional list of functions. Summary of representative groups of related functions identified by the different set of lentil tags. (XLSX 13 kb)
Overview of the heat stress conditions used in the study. (A) Pictograph showing the stress regim... more Overview of the heat stress conditions used in the study. (A) Pictograph showing the stress regime used for plant treatment as described in material and methods. (B) Representative photos of flower buds corresponding to different pollen stages. (C) Photos of pollen cells from different developmental stages, stained with the Alexander dye. Positive staining indicates viable pollen. (D) Bright field image of pollen at tetrad stage and fluorescent image of post-meiotic and mature pollen stained with DAPI, showing the single and double nuclei, respectively. (DOCX 2811 kb)
Novel putative miRNAs in post-meiotic pollen with their chromosomal position, mapping coordinates... more Novel putative miRNAs in post-meiotic pollen with their chromosomal position, mapping coordinates, sequence of the predicted miRNA precursor, star sequence, and mature sequence. (XLSX 71 kb)
Escherichia coli strain Nissle 1917 (EcN) is the active principle of a probiotic preparation (tra... more Escherichia coli strain Nissle 1917 (EcN) is the active principle of a probiotic preparation (trade name Mutaflor(®)) used for the treatment of patients with intestinal diseases such as ulcerative colitis and diarrhea. It has GRAS (generally recognized as save) status and has been shown to be a therapeutically effective drug (Sonnenborn and Schulze, 2009). The complete genomic DNA sequence will help in identifying genes and their products which are essential for the strains probiotic nature. Genbank/EMBL/DDBJ accession number: CP007799 (chromosome).
A 454-FLX low-coverage sequencing approach was used to assemble the mitochondrial genome of Radix... more A 454-FLX low-coverage sequencing approach was used to assemble the mitochondrial genome of Radix balthica. The mtDNA sequence is 13,993 nt long and contains 37 genes (13 protein coding genes, two rRNAs and 22 tRNAs). Four genes, the 12S RNA and seven tRNAs are transcribed in reverse order. The sequence is AT rich (71.3%), similar to other basommatophoran species. Comparison with the most closely related mt genomes available (Biomphalaria glabrata and Biomphalaria tenagophila) revealed identical gene orders except for five tRNAs. Next generation sequencing proved to be a fast and easy method for sequencing an entire mitochondrial genome.
PurposeTo investigate the expression profile of the hypoxia-inducible transcription factor-1α (HI... more PurposeTo investigate the expression profile of the hypoxia-inducible transcription factor-1α (HIF-1α) and its downstream targets in malignancies of the ocular adnexa and to determine its relevance as a prognostic factor for clinical outcome.MethodsWe included 49 subjects with malignant tumours (25 squamous cell carcinomas (SCC), 15 non-Hodgkin lymphomas, 9 melanomas) and 30 patients with benign tumours of the ocular adnexa (13 papillomas, 7 reactive lymphoid hyperplasias (RLHs) and 10 nevi) as controls. We quantified HIF-1α protein expression by immunohistochemistry and assessed the association between HIF-1α and clinical outcome via Kaplan–Meier analysis. Furthermore, we assessed the expression of HIF-1α downstream factors by transcriptional sequencing using the MACE (massive analysis of cDNA ends) technology.ResultsSCCs revealed a strong HIF-1α expression in 61% of tumour cells in comparison with only 22% in papillomas (p < 0.0001). In contrast, malignant melanomas and lymphom...
Trabajo presentado en el IV International Ascochyta Workshop (Ascochyta 2016), celebrado en Troia... more Trabajo presentado en el IV International Ascochyta Workshop (Ascochyta 2016), celebrado en Troia (Portugal) el 10 y 11 de octubre de 2016.
The novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19... more The novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19 which has become a global concern due to its rapid spread. Meanwhile, increased demand in testing has led to shortage of reagents, supplies, and compromised the performance of diagnostic laboratories in many countries. Both the world health organization (WHO) and the Center for Disease Control and Prevention (CDC) recommend multi-step RT-PCR assays using multiple primer and probe pairs, which might complicate interpretation of the test results especially for borderline cases. In this study, we describe an alternative RT-PCR approach for the detection of SARS-CoV-2 RNA that can be used for the probe-based detection of clinical isolates in the diagnostics as well as in research labs using a low cost SYBR green method. For the evaluation, we used samples from patients with confirmed SARS-CoV-2 infection and performed RT-PCR assays along with successive dilutions of RNA standards to determi...
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Papers by Klaus Hoffmeier