The close phylogenetic relationship of the important pathogen Streptococcus pneumoniae and several species of commensal streptococci, particularly Streptococcus mitis and Streptococcus pseudopneumoniae, and the recently demonstrated sharing of genes and phenotypic traits previously considered specific for S. pneumoniae hamper the exact identification of S. pneumoniae. Based on sequence analysis...

Histidine acid phytases (HAPhy) are widely distributed enzymes among bacteria, fungi, plants, and some animal tissues. They have a significant role as an animal feed enzyme and in the solubilization of insoluble phosphates and minerals present in the form of phytic acid complex. A set of 50 reference protein sequences representing HAPhy were retrieved from NCBI protein database and characterize...

Previously, we constructed the transfinite Goodwillie spectral sequence (TGSS), whose signature is roughly E t,J(S ) = πtS ⇒ πtS. This spectral sequence computes unstable homotopy from stable data. Over the next couple of talks, we’ll discuss the differentials in this spectral sequence, but for today, let’s just focus on understanding the relationship between the E page and the E∞ page at a hig...

Recent advances in sequencing technologies have enabled the production of massive amounts of data on somatic mutations from cancer genomes. These data have led to the detection of characteristic patterns of somatic mutations or "mutation signatures" at an unprecedented resolution, with the potential for new insights into the causes and mechanisms of tumorigenesis. Here we present new methods fo...

We have determined the crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 at 1.9 A resolution. This protein is a member of the Escherichia coli ygcH sequence family, which contains approximately 15 sequence homologs of bacterial origin. These homologs have a high isoelectric point. The crystal structure reveals that TTHB192 consists of two independently folded domai...

Proteins that share a similar function often exhibit conserved sequence patterns. Sequence patterns help to classify proteins into families where the exact function may or may not be known. Research has shown that these domain signatures often exhibit specific three-dimensional structures. We have previously shown that sequence patterns combined with structural information, in general, have sup...

Inwardly rectifying K+ channels or Kirs are a large gene family and have been predicted to have two transmembrane segments, M1 and M2, intracellular N and C termini, and two extracellular loops, E1 and E2, separated by an intramembranous pore-forming segment, H5. H5 contains a stretch of eight residues that are similar in voltage-dependent K+ channels, Kvs, and this stretch is called the signat...

Follicular lymphoma (FL) is an uncurable cancer characterized by progressive severity of relapses. We analyzed sequence context specificity of mutations in the B cells from a large cohort of FL patients. We revealed substantial excess of mutations within a novel hybrid nucleotide motif: the signature of somatic hypermutation (SHM) enzyme, Activation Induced Deaminase (AID), which overlaps the C...

Human nuclear RNase P purified from HeLa cells has ATPase activity. This activity is associated with one of the protein subunits of the enzyme, Rpp20. Thus, human nuclear RNase P, which contains several proteins and one essential RNA, has at least one other enzymatic activity in addition to cleavage of phosphoester bonds in RNA. The amino acid sequence of Rpp20 has a signature motif found in an...

condition monitoring of bldc motors due to their important applications is gaining more and more significance. rotor eccentricity is one of the most important sources of faults in these motors. up to now, detection methods of this fault under nonstationary conditions are limited to complicated and time-consuming methods using wavelets and cohen class algorithms which are difficult to implement ...