Perfect sorting by reversals is not always difficult

We propose new algorithms for computing pairwise rearrangement scenarios that conserve the combinatorial structure of genomes. More precisely, we investigate the problem of sorting signed permutations by reversals without breaking common intervals. We describe a combinatorial framework for this problem that allows us to characterize classes of signed permutations for which one can compute, in polynomial time, a shortest reversal scenario that conserves all common intervals. In particular, we define a class of permutations for which this computation can be done in linear time with a very simple algorithm that does not rely on the classical Hannenhalli-Pevzner theory for sorting by reversals. We apply these methods to the computation of rearrangement scenarios between permutations obtained from 16 synteny blocks of the X chromosomes of the human, mouse, and rat     

Deregulated expression of Cdc6 in the skin facilitates papilloma formation and affects the hair growth cycle

Cdc6 encodes a key protein for DNA replication, responsible for the recruitment of the MCM helicase to replication origins during the G1 phase of the cell division cycle. The oncogenic potential of deregulated Cdc6 expression has been inferred from cellular studies, but no mouse models have been described to study its effects in mammalian tissues. Here we report the generation of K5-Cdc6, a transgenic mouse strain in which Cdc6 expression is deregulated in tissues with stratified epithelia. Higher levels of CDC6 protein enhanced the loading of MCM complexes to DNA in epidermal keratinocytes, without affecting their proliferation rate or inducing DNA damage. While Cdc6 overexpression did not promote skin tumors, it facilitated the formation of papillomas in cooperation with mutagenic agents such as DMBA. In addition, the elevated levels of CDC6 protein in the skin extended the resting stage of the hair growth cycle, leading to better fur preservation in older mice.     

Can carbon credits fund riparian forest restoration?

Ecological restoration is increasingly called on to provide ecosystem services (ES) valuable to humans, as well as to benefit biodiversity and improve wildlife habitat. Where mechanisms to pay for ES exist, they may serve as incentives to embark on habitat restoration projects. We evaluated the potential of newly established carbon markets in the United States to incentivize afforestation along riparian corridors, by comparing the income earnable by carbon offset credits with the costs of planting, maintaining, and registering such a restoration project in California. We used a 20‐year chronosequence of riparian forest sites along the Sacramento River as our model project. We found that carbon credits can repay more than 100% of costs after two decades of regrowth, if sufficient effort is put into sampling intensity in the first post‐restoration decade. However, carbon credits alone are unlikely to entice landowners currently engaged in agricultural activities to switch from farming crops to farming habitat.     

Notes on the ant genus Cataglyphis Foerster, 1850 (Hymenoptera,Formicidae) in the Arabian Peninsula with description of a new species and a key to species of the C. pallida-group

Cataglyphis fisheri sp. n. is described and illustrated from the United Arab Emirates, Oman and Kingdom of Saudi Arabia based on the worker caste. It belongs to the Cataglyphis pallida-group which is recorded for the first time from the Arabian Peninsula. Cataglyphis fisheri sp. n. is similar to Cataglyphis pallida Mayr, 1877 from Kazakhstan. Differential diagnosis between these two species is given and a key to the species of the Cataglyphis pallida-group is presented. Cataglyphis laylae Collingwood, 2011 is treated as a junior synonym of Cataglyphis saharae Santschi, 1929. Cataglyphis flavobrunnea Collingwood & Agosti, 1996 is redescribed and a lectotype for this species is designated.     

New synonyms of two Arabian ants of the genus Monomorium Mayr, 1855 (Hymenoptera,Formicidae)

Synonymy of two Arabian Monomorium Mayr, 1855 species is proposed: Monomorium exiguum Forel, 1894 = Monomorium desertorum Collingwood & Agosti, 1996, syn. n.; Monomorium subopacum Smith, 1858 = Monomorium mintiribe Collingwood & Agosti, 1996, syn. n. A lectotype for Monomorium venustum Smith, 1858 is designated. Information on nesting habits of Monomorium exiguum and Monomorium venustum in the Kingdom of Saudi Arabia are provided for the first time. Recently collected records for Monomorium exiguum, Monomorium subopacum, and Monomorium venustum from the Kingdom of Saudi Arabia and United Arab Emirates are listed.     

HLA-DQA2 and HLA-DQB2 genes are specifically expressed in human Langerhans cells and encode a new HLA class II molecule

The precise role of human epidermal Langerhans cells (LCs) in immune response is highly controversial. While studying the gene expression profile of these cells, we were intrigued to identify the HLA-DQB2 gene as potentially expressed in LCs. Despite a strong evolutionary conservation of their sequences, the concomitant expression of the poorly polymorphic HLA-DQA2/HLA-DQB2 genes, paralogous to the HLA-DQA1/HLA-DQB1 genes, has never been detected in any cell type. We confirmed by RT-PCR that the HLA-DQA2 and -DQB2 genes are both expressed in LCs, but not in monocyte-derived dendritic cells, or in blood CD1c(+) or plasmacytoid dendritic cells. The presence of the HLA-DQβ2 chain in LCs could be demonstrated by Western blotting, whereas immunofluorescence revealed its localization in early endosomes. As in the case of other HLA class II molecules, the HLA-DQα2 and -DQβ2 chains formed heterodimers that had to associate with the invariant chain to reach endosomal compartments. HLA-DQα2/β2 heterodimers were expressed at the cell surface, where they could mediate staphylococcal superantigen stimulation of T cells. Interestingly, HLA-DQα2 and HLA-DQβ1 chains formed mixed heterodimers which efficiently left the endoplasmic reticulum. These observations strongly suggest that the poorly polymorphic HLA-DQA2 and -DQB2 genes should be considered to be of immunological importance. The HLA-DQα2/β2 molecules could influence the complexity of the repertoire of Ags presented by LCs.     

The Archaeal Proteasome Is Regulated by a Network of AAA ATPases

The proteasome is the central machinery for targeted protein degradation in archaea, Actinobacteria, and eukaryotes. In its basic form, it consists of a regulatory ATPase complex and a proteolytic core particle. The interaction between the two is governed by an HbYX motif (where Hb is a hydrophobic residue, Y is tyrosine, and X is any amino acid) at the C terminus of the ATPase subunits, which stimulates gate opening of the proteasomal α-subunits. In archaea, the proteasome-interacting motif is not only found in canonical proteasome-activating nucleotidases of the PAN/ARC/Rpt group, which are absent in major archaeal lineages, but also in proteins of the CDC48/p97/VAT and AMA groups, suggesting a regulatory network of proteasomal ATPases. Indeed, Thermoplasma acidophilum, which lacks PAN, encodes one CDC48 protein that interacts with the 20S proteasome and activates the degradation of model substrates. In contrast, Methanosarcina mazei contains seven AAA proteins, five of which, both PAN proteins, two out of three CDC48 proteins, and the AMA protein, function as proteasomal gatekeepers. The prevalent presence of multiple, distinct proteasomal ATPases in archaea thus results in a network of regulatory ATPases that may widen the substrate spectrum of proteasomal protein degradation.