PubMed Health⌕ Search

Biomedical subjects

Daniel Fischer

Publications and source records attributed to Daniel Fischer.

24 records · Page 2Linked to original sources
PubMed2003

Twenty thousand ORFan microbial protein families for the biologist?

The genomes of most newly sequenced organisms contain a significant fraction of ORFs (open reading frames) that match no other sequence in the databases. We refer to these singleton ORFs as sequence ORFans. Because little can be learned about ORFans by homology, the origin and functions of ORFans remain a mystery. However, in this era of full genome sequencing, it seems that ORFans have been underemphasized. In this minireview, we draw attention to the increasing number of ORFans and to the consequences of this growth to biological research in the postgenomic era.

Animals↗
PubMed2003

The 2002 Olympic Games of protein structure prediction.

The summer of every even year is considered by the protein structure prediction community as the Olympic Games season, because in addition to a number of continuous benchmarking experiments such as LiveBench, much effort is invested in the blind prediction experiments CASP and CAFASP. Here we report the major advances registered in the field since the last Games of 2000, as measured by the recently completed LiveBench-4 experiment. These results provide a timely measure of the capabilities of current methods and of their expected performance in the upcoming CASP-5 and CAFASP-3 experiments. We also describe the initiation of the two new, community-wide experiments, PDB-CAFASP and MR-CAFASP. These new experiments extend the scope of previous efforts and may have important implications for structural genomics.

Computational Biology↗
PubMedDate not supplied

Microbial desizing using starch as model compound: enzyme properties and desizing efficiency.

A film of sizing agents protects yarn during weaving. Its removal in a subsequent washing process causes 50% of the organic effluent load of textile finishing processes and requires large amounts of auxiliary chemicals (e.g., surfactants). Microbial desizing is a new bioprocess that uses the acidifying culture of a two-phase anaerobic digestion plant for the removal and partial degradation (acidification) of the sizing agent. Soluble starch is used in this study to characterize the enzymatic properties in the supernatant of the desizing culture and to link them to desizing efficiencies. The supernatant of the culture (grown at 37 degrees C, pH 5.5) displayed the highest enzymatic activity between pH 4 and 5 and in a broad temperature range (20-80 degrees C). Highest metabolization rates were determined with the substrate amylose. Short chain dextrins (average of 5 and 10 glucose units) and amylopectin were converted significantly more slowly. At 37 degrees C the half-life time of the enzymatic activity in the supernatant was 45 h. In a desizing test a decisive reduction of the chain length was found already after 1 h (allowing starch solubilization). A microbial desizing experiment with dyed, native maize starch demonstrated the efficiency of the proposed bioprocess.

Bacteria, Anaerobic↗