The classification performance of Kraken was evaluated in terms of sensitivity and specificity when using short and long 16S rRNA sequences. A total of 440,738 sequences from bacteria with complete taxonomic classifications were downloaded from the high quality ribosomal RNA database SILVA. Amplicons produced (86,371 sequences; 1450 bp) by virtual PCR with primers covering the V1-V9 region of t...

Humanized monoclonal antibody KD-247 targets the Gly(312)-Pro(313)-Gly(314)-Arg(315) arch of the third hypervariable (V3) loop of the HIV-1 surface glycoprotein. It potently neutralizes many HIV-1 clade B isolates, but not of other clades. To understand the molecular basis of this specificity, we solved a high-resolution (1.55 Å) crystal structure of the KD-247 antigen binding fragment and exam...

BACKGROUND AND PURPOSE MR imaging is the method of choice for evaluating the trigeminal nerve. Detection of abnormalities such as perineural tumor spread requires detailed knowledge of the normal MR appearance of the trigeminal nerve and surrounding structures. The purpose of this study was to clarify the normal MR appearance and variations of the trigeminal ganglion, maxillary nerve (V2), and ...

AIM To investigate the role of a novel dipeptidyl peptidase 8 transcript variant (DPP8-v3) gene in testis development and/or spermatogenesis. METHODS A human testis cDNA microarray was hybridized with mRNA of human adult and fetal testes. Differentially expressed clones were sequenced and characterized and their expression was analyzed by real-time reverse transcription polymerase chain react...

Human immunodeficiency virus type 1 (HIV-1) coreceptor usage and tropism can be modulated by the V3 loop sequence of the gp120 exterior envelope glycoprotein. For coreceptors, R5 viruses use CCR5, X4 viruses use CXCR4, and dual-tropic (R5X4) viruses use either CCR5 or CXCR4. To understand the requirements for dual tropism, we derived and analyzed a dual-tropic variant of an X4 virus. Changes in...

Once relegated to mundane roles as glue logic—linking the CPUs, memory and I/O in computerbased systems—field-programmable gate arrays are moving into prime time. Today’s leading FPGA products boast multi-million gate counts, I/O pins in the high hundreds and true system chip-level functionality including embedded CPUs. As they continue to bulk up in all these directions, they’re evolving into ...

Feline immunodeficiency virus (FIV) shares with T-cell tropic strains of human immunodeficiency virus type 1 (HIV-1) the use of the chemokine receptor CXCR4 for cellular entry. In order to map the interaction of the FIV envelope surface unit (SU) with CXCR4, full-length FIV SU-Fc as well as constructs with deletions of extended loop L2, V3, V4, or V5 were produced in stable CHO cell lines. Bind...

Background The V3 loop of the env gene in HIV-C type is considered as a major viral determinant for coreceptor specificity. The tip motif of v3 loop is known for antibody neutralization, so sequence variation in this motif have an impact on virus infectivity and disease progression. So analysis of genetic diversity in the V3 loop Tip motif help us to improve the CCR5 antagonist’s development as...

Aim: The objects of this study originated from the experimental observations, whereby the HIV -1 gp120 V3 loop is a high-affinity ligand for immunophilins, and consisted in generating the structural complex of cyclophilin (Cyc) B belonging to immunophilins family with the virus subtype A V3 loop (SA-V3 loop) as well as in specifying the Cyc B segment forming the binding site for V3 synthetic co...