Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and bacteria. Researchers increasingly depend on the outputs of these tools to infer transmission dynamics of human diseases and make actionable recommendations to public health officials (Black et al., 2020; Gardy et al., 2015). In order to enable real-time analyses of pathogen evolution, bioinformatics tools must scale rapidly with the number of samples and be flexible enough to adapt to a variety of questions and organisms. To meet these needs, we developed Augur, a bioinformatics toolkit designed for phylogenetic analyses of human pathogens

Isolation and individual electrical stimulation of single smooth-muscle cells from the urinary bladder of the pig

In contrast to striated muscle, measurements on strips of smooth muscle cannot be uniquely interpreted in terms of an array of contractile units. Therefore scaling down to the single-cell level is necessary to gain detailed understanding of the contractile process in this type of muscle. The present study describes the development of a method for isolating contractile single smooth muscle cells from pig urinary bladders. Contractile responses evoked by individual electrical stimulation were used as a measure of cell quality during development of the method. Responses were evaluated by measuring latency, contraction and relaxation times, as indicated by visible length changes, and stored on-line in a computer. Initial length, relative shortening and shortening speed were determined by measuring cell lengths in previously timed still video frames using a computer-controlled crosshair device. Increase of stimulus pulse duration resulted in improved responses, indicating that the observed shortening represented a physiological contractile response. Ultimately this method of evaluation was applied to two sets of cell preparations obtained by two different methods, one using only collagenase digestion, the other using mechanical manipulation as well. Both sets showed two main patterns of response to electrical stimulation: a pattern of contraction upon stimulation followed by enhanced contraction when stimulation was switched off (CK), and a pattern of contraction upon stimulation followed by relaxation when the stimulus was switched off (CR). The set of preparations containing the highest percentage of CR cells was found to be superior (i.e. greater initial length, shorter latency and contraction times, increased shortening and higher shortening speed). The method of isolation used for this set gives a high yield of contractile cells available for experimental use over a long span of time

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo

What do functionally important DNA sites, those scrutinized and shaped by natural selection, tell us about the place of humans in evolution? Here we compare ≈90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. On a time scale, the coding DNA divergencies separate the human–chimpanzee clade from the gorilla clade at between 6 and 7 million years ago and place the most recent common ancestor of humans and chimpanzees at between 5 and 6 million years ago. The evolutionary rate of coding DNA in the catarrhine clade (Old World monkey and ape, including human) is much slower than in the lineage to mouse. Among the genes examined, 30 show evidence of positive selection during descent of catarrhines. Nonsynonymous substitutions by themselves, in this subset of positively selected genes, group humans and chimpanzees closest to each other and have chimpanzees diverge about as much from the common human–chimpanzee ancestor as humans do. This functional DNA evidence supports two previously offered taxonomic proposals: family Hominidae should include all extant apes; and genus Homo should include three extant species and two subgenera, Homo (Homo) sapiens (humankind), Homo (Pan) troglodytes (common chimpanzee), and Homo (Pan) paniscus (bonobo chimpanzee)

Initial Experience Treating Lung Tumors with the CyberKnife

Stereotactic body radiosurgery (SBRS) of lung tumors with the CyberKnife® (Accuray Incorporated, Sunnyvale, CA) achieves excellent rates of local disease control with limited toxicity to surrounding tissues. We retrospectively reviewed treatments and outcomes for 90 patients with 109 lung lesions treated at the CyberKnife Center of Miami between March 2004 and September 2006. This monotherapy review included 49 patients with 53 primary lung cancers, 27 patients with 42 pulmonary metastases, 6 patients with external beam failure and 8 patients treated by SBRS as a boost following or before conventionally fractionated radiotherapy (3DCRT or IMRT). In the primary tumor category, 43 patients remain alive. Thirty-two have been followed 1 to 25 months (median = 11.5 months). Fortynine percent (21/43) of them have had a complete radiographic response and have been followed for a median of 18.5 months. Another 8 have evidence of at least a partial radiographic response. There have been 5 failures (5/43) within the PTV, for a local recurrence rate of 11%. Of the total 109 treated lesions, 97/109 (89%) showed radiographic evidence of at least a partial response to treatment. Six of the failures were in lesions 100 cc. All of the patients tolerated SBRS well with fatigue as the main toxicity. Two patients required hospitalization for Grade III radiation pneumonitis. We conclude that the delivery of precisely targeted, high dose, hypofractionated irradiation to lung tumors with the CyberKnife is well tolerated and has outcomes that are comparable with published results for other methods of SBRS