Minerals in Afghanistan : gemstones of Afghanistan

Afghanistan and gemstones have been inextricably linked for 6500 years and the country remains rich in precious and semiprecious gemstone deposits (Figure 1). Lapis lazuli, mined in the Hindu Kush since the Neolithic Period, was transported along the ancient trade routes to Mesopotamia, Ur, Egypt and India. Precious gems including emeralds, ruby and sapphires (Figure 2) are mined in Afghanistan, and semi-precious lapis lazuli, tourmaline, aquamarine, kunzite, topaz, garnets, fluorite and varieties of quartz are also worked. Afghanistan is also a source of good quality mineral specimens sought by collectors. Gemstone mining in Afghanistan is typically an artisanal activity, carried out by people living in villages surrounding the mines. Tunnels are excavated and gems are extracted by hand using drills, dynamite and often high explosives recycled from ordnance. These techniques lead to much waste and damage to gems, and result in low yield. Most of the gemstones mined in Afghanistan leave the country illicitly, 90–95 % of them going to Peshawar in Pakistan where they are sorted for quality

Interplay between DNA sequence and negative superhelicity drives R-loop structures.

R-loops are abundant three-stranded nucleic-acid structures that form in cis during transcription. Experimental evidence suggests that R-loop formation is affected by DNA sequence and topology. However, the exact manner by which these factors interact to determine R-loop susceptibility is unclear. To investigate this, we developed a statistical mechanical equilibrium model of R-loop formation in superhelical DNA. In this model, the energy involved in forming an R-loop includes four terms-junctional and base-pairing energies and energies associated with superhelicity and with the torsional winding of the displaced DNA single strand around the RNA:DNA hybrid. This model shows that the significant energy barrier imposed by the formation of junctions can be overcome in two ways. First, base-pairing energy can favor RNA:DNA over DNA:DNA duplexes in favorable sequences. Second, R-loops, by absorbing negative superhelicity, partially or fully relax the rest of the DNA domain, thereby returning it to a lower energy state. In vitro transcription assays confirmed that R-loops cause plasmid relaxation and that negative superhelicity is required for R-loops to form, even in a favorable region. Single-molecule R-loop footprinting following in vitro transcription showed a strong agreement between theoretical predictions and experimental mapping of stable R-loop positions and further revealed the impact of DNA topology on the R-loop distribution landscape. Our results clarify the interplay between base sequence and DNA superhelicity in controlling R-loop stability. They also reveal R-loops as powerful and reversible topology sinks that cells may use to nonenzymatically relieve superhelical stress during transcription

Divergence history of the Rufous-tailed Tailorbird (Orthotomus sericeus) of Sundaland: Implications for the biogeography of Palawan and the taxonomy of island species in general

The Rufous-tailed Tailorbird (Orthotomus sericeus)—a Sunda endemic—is divided into 3 morphologically based subspecies: one in western Sundaland (Malay Peninsula, Sumatra, and associated islands), one from the Natuna Islands in the South China Sea, and one on Borneo, Palawan, and smaller islands of the Sunda continental shelf east of Borneo. Previous study, however, suggested that these subspecies do not conform to molecular genetic subdivisions of the species. We reexamined the morphology and performed molecular phylogeographic and multi-locus coalescent analysis of two subspecies of Rufous-tailed Tailorbird comprising populations on the Malay Peninsula, Sumatra, Borneo, and Palawan. We found (1) little morphological difference among the two subspecies, (2) no substantial genetic differences between the Borneo and western Sunda populations, but (3) marked genetic divergence between the Palawan and other populations. We conclude that the Bornean and western Sunda populations interbred extensively during Quaternary glacio-eustatic land connections, whereas the Bornean and Palawan populations did not. Unlike the other Greater Sunda Islands, Palawan has not been attached by a land bridge to the rest of Sundaland for at least one million years, and its relative isolation has prevented extensive intermixing between Palawan's and other Sunda populations. Thus, the Palawan population appears to be on its own evolutionary trajectory. The ability to demonstrate extensive interbreeding among some Sunda island populations, but not others, illustrates the practicality of testing Gill's (2014) “null hypothesis” that morphologically distinct populations on different islands are different species unless a compelling argument can be made to the contrary. In this case, Rufous-tailed Tailorbird morphology provided little or misleading evidence of the extent of interbreeding, whereas modern genetic analysis provided a clear view