Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR.

During HIV-1 assembly, the viral Gag polyprotein specifically selects the dimeric RNA genome for packaging into new virions. The 5' untranslated region (5'UTR) of the dimeric genome may adopt a conformation that is optimal for recognition by Gag. Further conformational rearrangement of the 5'UTR, promoted by the nucleocapsid (NC) domain of Gag, is predicted during virus maturation. Two 5'UTR dimer conformations, the kissing dimer (KD) and the extended dimer (ED), have been identified in vitro, which differ in the extent of intermolecular basepairing. Whether 5'UTRs from different HIV-1 strains with distinct sequences have access to the same dimer conformations has not been determined. Here, we applied fluorescence cross-correlation spectroscopy and single-molecule Förster resonance energy transfer imaging to demonstrate that 5'UTRs from two different HIV-1 subtypes form (KDs) with divergent stabilities. We further show that both 5'UTRs convert to a stable dimer in the presence of the viral NC protein, adopting a conformation consistent with extensive intermolecular contacts. These results support a unified model in which the genomes of diverse HIV-1 strains adopt an ED conformation.

Correction: Barcoding Eophila crodabepis sp. nov. (Annelida, Oligochaeta, Lumbricidae), a Large Stripy Earthworm from Alpine Foothills of Northeastern Italy Similar to Eophila tellinii (Rosa, 1888).

[This corrects the article DOI: 10.1371/journal.pone.0151799.].

A comprehensive checklist of earthworm species and subspecies from Vietnam (Annelida: Clitellata: Oligochaeta: Almidae, Eudrilidae, Glossoscolecidae, Lumbricidae, Megascolecidae, Moniligastridae, Ocnerodrilidae, Octochaetidae).

The comprehensive checklist of earthworms in Vietnam is presented here listing 24 genera and 212 species arranged in eight families. For each species, bibliographic citations are given, including the original descriptions as well as notable citations affecting taxonomic status or distributional reports of a species. Distributions of each species are also provided. The bibliography contains all relevant papers for Vietnamese earthworms. Of 212 species, 114 have been recorded only in Vietnam, and 25 are cosmopolitan. New combinations are made for Amynthas acalifornicus (Do & Huynh, 1991) comb. nov., A. binhgiaensis (Le, 1994) comb. nov., Metaphire catbaensis (Thai & Le, 1993) comb. nov., M. khoii (Do & Tran, 1994) comb. nov., M. phaluongana (Do & Huynh, 1992) comb. nov., and M. mangophila (Nguyen, 2011) comb. nov., M. tripidoporophoratus (Thai & Nguyen, 1993) comb. nov. Additionally, Pheretima paraalexandri Nguyen, 2011 is treated as a junior synonym of Amynthas polychaetiferus (Thai, 1984).

Barcoding Eophila crodabepis sp. nov. (Annelida, Oligochaeta, Lumbricidae), a Large Stripy Earthworm from Alpine Foothills of Northeastern Italy Similar to Eophila tellinii (Rosa, 1888).

A new Italian earthworm morphologically close to the similarly large and anecic Eophila tellinii (Rosa, 1888) is described. Distribution of Eophila crodabepis sp. nov. extends over 750 km2 from East to West on the Asiago Plateau and Vittorio Veneto Hills, from North to South on mounts Belluno Prealps (Praderadego and Cesen), Asiago, Grappa and onto the Montello foothills. This range abuts that of Eophila tellinii in northern Friuli Venezia Giulia region. Known localities of both E. tellinii and E. crodabepis sp. nov. are mapped. mtDNA barcoding definitively separates the new western species from classical Eophila tellinii (Rosa, 1888).

Two new Korean earthworms (Annelida, Oligochaeta, Megadrilacea, Megascolecidae).

Two Korean endemic pheretimoid Amynthas Kinberg, 1867 species belonging in family Megascolecidae s. stricto are sketched, dissected and described. Amynthas daeari Blakemore sp. n. has spermathecae in 6/7/8 complying with an Amynthas tokioensis spp-group, whilst Amynthas jinburi Blakemore sp. n. has spermathecal pores in 5 & 6 strictly complying with Sims and Easton's (1972)Amynthas canaliculatus-group. A definitive COI gene barcode is provided for the holotype of Amynthas daeari but the age since collection or preservation of the Amynthas jinburi type in 2000 precluded its mtDNA extraction at this time.

Earthworms newly from Mongolia (Oligochaeta, Lumbricidae, Eisenia).

Two new megadrile earthworms from the steppes, the first species wholly from Outer Mongolia, are ascribed to the partially parthenogenetic Eisenia nordenskioldi (Eisen, 1879) species-complex. Taxonomic justification of sympatric Eisenia nordenskioldi mongol and Eisenia nordenskioldi onon ssp. n. are supported by mtDNA COI barcodes. The unreliability of molecular differentiation based on voucher names compared to definitive types is again demonstrated, as pertains to the ultimate Eisenia andrei Bouché, 1972 synonym of the Eisenia fetida (Savigny, 1826) sibling species-complex composed of more than a dozen prior names. Similar species described from Northeast China [formerly Manchuria] and North Korea are briefly considered, albeit they are intermittently held in synonymy of cosmopolitan Aporrectodea rosea (Savigny, 1826) along with many other taxa including some exotic lumbricids initially found in India. Japanese and North American lumbricids are also mentioned. Distributions are discussed and an annotated checklist of all nine Siberian/sub-arctic Eisenia nordenskioldi ssp. is appended.