Forum: the prison reentry industry

This forum addresses the emerging Prison Reentry Industry (PRI).  It features articles and essays from authors on three continents, and from a variety of perspectives.  The authors included here range from ex-prisoners and current prisoners, PRI workers and activists, former prisoners now involved in academic and policy research, critics and practitioners.  Together these essays mark a first effort to bring a number of perspectives to bear on a growing and already vast array of programs, in the United States and beyond.  From these perspectives, the hope is that the criticism brought forward here will help stimulate debate and reform in future discussions about a processes that affect the lives of millions of people world-wide.     

Molecular divergence in the Galapagos Islands—Baja California species pair,Gossypium klotzschianum andG. davidsonii (Malvaceae)

Molecular divergence betweenGossypium klotzschianum andG. davidsonii was studied. The former is endemic to five of the larger islands of the Galapagos, whileG. davidsonii is restricted to the southern half of Baja California, approximately 2 500 km distant. A substantial body of genetic and taxonomic data suggests that these two species are related as progenitor and derivative. Interspecific hybrids are fully fertile, with no evidence of F₂ breakdown and normal segregation of genetic markers. Allozyme analysis of 33 populations for 41 loci indicated that the allelic composition ofG. klotzschianum represents a subset ofG. davidsonii. Although genetic diversity is relatively restricted in both species, calculated measures demonstrate higher levels of genetic variability and greater population structuring inG. davidsonii than inG. klotzschianum. The interspecific genetic identity of 0.87 is typical for progenitor-derivative species pairs. Chloroplast DNAs were surveyed for variation with 25 restriction enzymes using hybridization probes that cover the entire chloroplast genome. No intraspecific and little interspecific variation was detected among 560 cpDNA restriction sites, representing sequence information for approximately 3200 nucleotides. Only 3 mutational differences distinguished the two species, resulting in a sequence divergence estimate of 0.09%. Divergence times were estimated from both the isozyme data and the cpDNA restriction site data. Although these estimates have several sources of error, both molecular data sets were congruent in suggesting that the two lineages diverged between 250000 and 700000 years ago. Accumulated evidence suggests that dispersal was from Baja California to the Galapagos Islands rather than the reverse, and most likely was mediated by trans-oceanic drift.G. klotzschianum may be the only species of the endemic Galapagos flora to have arisen from a northern Mexican progenitor.     

The legacy of diploid progenitors in allopolyploid gene expression patterns

Allopolyploidization (hybridization and whole-genome duplication) is a common phenomenon in plant evolution with immediate saltational effects on genome structure and gene expression. New technologies have allowed rapid progress over the past decade in our understanding of the consequences of allopolyploidy. A major question, raised by early pioneer of this field Leslie Gottlieb, concerned the extent to which gene expression differences among duplicate genes present in an allopolyploid are a legacy of expression differences that were already present in the progenitor diploid species. Addressing this question necessitates phylogenetically well-understood natural study systems, appropriate technology, availability of genomic resources and a suitable analytical framework, including a sufficiently detailed and generally accepted terminology. Here, we review these requirements and illustrate their application to a natural study system that Gottlieb worked on and recommended for this purpose: recent allopolyploids of Tragopogon (Asteraceae). We reanalyse recent data from this system within the conceptual framework of parental legacies on duplicate gene expression in allopolyploids. On a broader level, we highlight the intellectual connection between Gottlieb''s phrasing of this issue and the more contemporary framework of cis- versus trans-regulation of duplicate gene expression in allopolyploid plants.     

Oligonucleotide primers for specific detection of actinobacterial laccases from superfamilies I and K

Although many putative laccase-like genes have been assigned to members of the phylum Actinobacteria, few of the related enzymes have been characterized so far. It is noteworthy, however, that this small number of enzymes has presented properties with industrial relevance. This observation, combined with the recognized biotechnological potential and the capability of this phylum to degrade recalcitrant soil polymers, has attracted attention for bioprospective approaches. In the present work, we have designed and tested primers that were specific for detection of sub-groups of laccase-like genes within actinomycetes, which corresponded to the superfamilies I and K from the classification presented by the laccase and multicopper oxidase engineering database. The designed primers have amplified laccase-like gene fragments from actinomycete isolates that were undetectable by primers available from the literature. Furthermore, phylogenetic alignments suggest that some of these fragments may belong to new laccases-like proteins, and thus emphasize the benefits of designing subgroup-specific primers.     

Ecohealth as a Field: Looking Forward

This forum paper proposes a reflection on the “field of ecohealth” and on how best to sustain a supportive environment that enables the evolution of diverse partnerships and forms of collaboration in the field. It is based on the results of a preconference workshop held in October 2012, in Kunming, China at the fourth biennial conference of the International Association for Ecology and Health. Attended by 105 persons from 38 countries, this workshop aimed to have a large-group and encompassing discussion about ecohealth as an emerging field, touching on subjects such as actors, processes, structures, standards, and resources. Notes taken were used to conduct a qualitative thematic analysis combined with a semantic network analysis. Commonalities highlighted by these discussions draw a portrait of a field in which human health, complex systems thinking, action, and ecosystem health are considered central issues. The need to reach outside of academia to government and the general public was identified as a shared goal. A disconnect between participants’ main concerns and what they perceived as the main concerns of funding agencies emerged as a primary roadblock for the future.     

Sequencing and Utilization of the Gossypium Genomes

Revealing the genetic underpinnings of cotton productivity will require understanding both the prehistoric evolution of spinnable fibers, and the results of independent domestication processes in both the Old and New Worlds. Progress toward a reference sequence for the smallest Gossypium genome is a logical stepping-stone toward revealing diversity in the remaining seven genomes (A, B, C, E, F, G, K) that permitted Gossypium species to adapt to a wide range of ecosystems in warmer arid regions of the world, and toward identifying the emergent properties that account for the superior productivity and quality of tetraploid cottons. The greatest challenge facing the cotton community is not genome sequencing per se but the conversion of sequence to knowledge.     

Recombinantly produced hydrophobins from fungal analogues as highly surface-active performance proteins

Hydrophobins are available from natural resources only in milligram amounts. BASF succeeded in a recombinant production process, up-scaled to pilot plant production in kilogram scale. Strain and protein optimization by modulation of gene expression and generation of fusion proteins finally leads to two class I hydrophobins called H*Protein A and H*Protein B. By analytical ultracentrifugation, we confirm that the self-association of H*Proteins in solution is governed by their sequence, because oligomerization is induced by the same mechanisms (pH > 6, temperature ≫ 5°C, concentration > 0.2 mg/ml) as for the well-known native hydrophobins SC3 and HFB II. Additionally, we established the triggering of structure formation by bridging with divalent ions and the stabilization of dimers and tetramers by monovalent ions or surfactants. This interplay with surfactants can be exploited synergistically: The capacity for emulsification of a 300 ppm standard surfactant solution is boosted from 0 to 100% by the addition of a mere 1 ppm of our new hydrophobins, with H*Protein A and H*Protein B having specific application profiles. This astonishing performance is rationalized by the finding that the same minute admixtures enhance significantly the interfacial elastic modulus, thus stabilizing interfaces against coalescence and phase separation.