Algorithm for cellular reprogramming.

The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology. With data-guided frameworks we can develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. Here we describe an approach for optimizing the use of transcription factors (TFs) in cellular reprogramming, based on a device commonly used in optimal control. We construct an approximate model for the natural evolution of a cell-cycle-synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points during the cell cycle. To arrive at a model of moderate complexity, we cluster gene expression based on division of the genome into topologically associating domains (TADs) and then model the dynamics of TAD expression levels. Based on this dynamical model and additional data, such as known TF binding sites and activity, we develop a methodology for identifying the top TF candidates for a specific cellular reprogramming task. Our data-guided methodology identifies a number of TFs previously validated for reprogramming and/or natural differentiation and predicts some potentially useful combinations of TFs. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes.

Taxonomic revision of the ornate skink (Oligosoma ornatum; Reptilia: Scincidae) species complex from northern New Zealand.

Although the New Zealand skink fauna is known to be highly diverse, a substantial proportion of the recognised species remain undescribed. We completed a taxonomic revision of the ornate skink (Oligosoma ornatum (Gray, 1843)) as a previous molecular study indicated that it represented a species complex. As part of this work we have resolved some nomenclatural issues involving this species and a similar species, O. aeneum (Girard, 1857). A new skink species, Oligosoma roimata sp. nov., is described from the Poor Knights Islands, off the northeast coast of the North Island of New Zealand. This species is diagnosed by a range of morphological characters and genetic differentiation from O. ornatum. The conservation status of the new taxon appears to be of concern as it is endemic to the Poor Knights Islands and has rarely been seen over the past two decades.

Rationale for vertical periodontal defects being a contraindication to the socket-shield technique.

Much has been published on the socket-shield technique since its introduction to implant dentistry in 2010. The literature reports the technique to be a viable treatment option. Investigations should hence focus on improving the treatment, identifying pitfalls, and better educating clinicians. The technique has been advised as contraindicated at tooth roots with periodontal defects. The present case report aims to illustrate the additional risk and why intrabony periodontal defects may be a contraindication to this already challenging treatment.

Oligosoma aureocola sp. nov. (Reptilia: Scincidae) from the northern Southland high country of Aotearoa/New Zealand.

A species of diurnal skink from the Mataura Range and Mid Dome in central northern Southland, Aotearoa/New Zealand is described as Oligosoma aureocola sp. nov. It is a small species, coloured mid- to dark brown with smooth longitudinal stripes, and lives along rocky alpine ridges, low-stature shrublands, and tussock grasslands. This skink is a conspicuous species, easily sighted basking and foraging in talus or alpine plants such as golden spear grass (Aciphylla aurea).

A new alpine skink species (Scincidae: Eugongylinae: Oligosoma) from Kahurangi National Park, New Zealand.

A new species of Oligosoma is described from a slate scree in montane tussock grassland in Kahurangi National Park, New Zealand, where it is currently known from a single small site. The new species (Oligosoma kahurangi sp. nov.) can be distinguished from all congeners by its extremely long tail, 36-38 mid-body scale rows, head length/head width ratio of 1.66, and colour pattern. It is part of the O. longipes Patterson species complex. The species is currently very poorly known but likely to be highly threatened, and we suggest listing as Nationally Critical (Data Poor, One Location) in New Zealand, and Data Deficient in the IUCN red-list. Predation by introduced mammals, particularly mice, is assumed to be a threat to its survival.

A new species of Oligosoma (Squamata: Scincidae) from the northern North Island, New Zealand.

New Zealand is home to a diverse cool temperate assemblage of skinks, with 60+ identified taxa (genus Oligosoma Girard), of which only 50 have been formally described. Here we describe a new species (Oligosoma kakerakau sp. nov.) from Bream Head Scenic Reserve, near Whangrei Heads, Northland. This species is considered to be conspecific with a single specimen (Oligosoma Whirinaki) previously reported (in 2003) from Whirinaki Te Pua-a-Tne Conservation Park ~370 km further south. Oligosoma kakerakau sp. nov. can be distinguished from all other members of the genus by a combination of a distinctive teardrop marking below the eye, a distinctive mid-lateral stripe, and the colouration and pattern on its ventral surface. Our phylogenetic analyses indicate that Oligosoma kakerakau sp. nov. is most closely related to O. zelandicum (Gray), and more distantly to O. striatum (Buller) and O. homalonotum (Boulenger). Sea level changes during the Pliocene, such as the formation of the Manawat Strait, may have contributed to the divergence between Oligosoma kakerakau sp. nov. and O. zelandicum. We discuss the distribution, ecology and conservation of Oligosoma kakerakau sp. nov., and outline future research and conservation priorities for the species.

Lost and Found: Taxonomic revision of the speckled skink (Oligosoma infrapunctatum; Reptilia; Scincidae) species complex from New Zealand reveals a potential cryptic extinction, resurrection of two species, and description of three new species.

New Zealand has a diverse skink fauna, comprising 45 described native species, and at least 15 undescribed taxa, within the single genus Oligosoma Girard, 1857. One of the earliest described, and best known, species is the speckled skink, Oligosoma infrapunctatum (Boulenger 1887). Despite a relatively stable taxonomic history for nearly 114 years, recent molecular work has indicated that O. infrapunctatum represents a species complex, comprising numerous genetically divergent, range restricted taxa. We completed the first stage of a taxonomic revision of O. infrapunctatum, conducting a morphological re-evaluation of existing voucher material, and newly collected specimens, and generated a molecular phylogeny for the species complex. This allowed us to distinguish six species: O. infrapunctatum, two species resurrected from synonymy (O. newmani, O. robinsoni), and three new species (O. salmo sp. nov., O. albornense sp. nov. O. auroraensis sp. nov.). The name bearing type population of O. infrapunctatum has not been located again for at least 130 years: it remains to be rediscovered and may already be extinct. Two of the six species here are considered 'Nationally Critical' (O. albornense sp. nov., O. salmo sp. nov.) under the New Zealand Threat Classification System, the others are Nationally Vulnerable (O. auroraensis sp. nov.) and At Risk-Relict (O. newmani, O. robinsoni). Further taxonomic work will be required to determine the taxonomy of other speckled skink genetic lineages in the South Island, particularly O. aff. infrapunctatum "cobble", O. "Hokitika", O. "Southern North Island" and O. "Westport".

A new species of scincid lizard in the genus Oligosoma (Reptilia: Scincidae) from the mid-Canterbury high country, New Zealand.

New Zealand has a diverse, endemic skink fauna, which is recognised as the most species rich skink assemblage of any cool temperate region on earth. All native New Zealand skink species are assigned to a single genus, Oligosoma Girard. A new species of Oligosoma is described from screes in montane tussock grassland in the mid-Canterbury high country, New Zealand, where it is currently known from four sites on two mountain ranges. The new species (Oligosoma hoparatea sp. nov.) can be distinguished from all congeners by a combination of mid-body scale row and lamellae counts, scale morphologies, and a bold striped pattern with smooth-edged, dark lateral bands. It is part of the O. longipes Patterson species complex, and occurs in sympatry with its closest relative, O. aff. longipes 'southern'. The species is currently highly threatened, and is listed as Nationally Critical in New Zealand. Predation by a suite of introduced mammals is assumed to be a major threat to its survival.

Nucleome Analysis Reveals Structure-Function Relationships for Colon Cancer.

Chromosomal translocations and aneuploidy are hallmarks of cancer genomes; however, the impact of these aberrations on the nucleome (i.e., nuclear structure and gene expression) is not yet understood. Here, the nucleome of the colorectal cancer cell line HT-29 was analyzed using chromosome conformation capture (Hi-C) to study genome structure, complemented by RNA sequencing (RNA-seq) to determine the consequent changes in genome function. Importantly, translocations and copy number changes were identified at high resolution from Hi-C data and the structure-function relationships present in normal cells were maintained in cancer. In addition, a new copy number-based normalization method for Hi-C data was developed to analyze the effect of chromosomal aberrations on local chromatin structure. The data demonstrate that at the site of translocations, the correlation between chromatin organization and gene expression increases; thus, chromatin accessibility more directly reflects transcription. In addition, the homogeneously staining region of chromosome band 8q24 of HT-29, which includes the MYC oncogene, interacts with various loci throughout the genome and is composed of open chromatin. The methods, described herein, can be applied to the assessment of the nucleome in other cell types with chromosomal aberrations.Implications: Findings show that chromosome conformation capture identifies chromosomal abnormalities at high resolution in cancer cells and that these abnormalities alter the relationship between structure and function. Mol Cancer Res; 15(7); 821-30. ©2017 AACR.