Large-scale medieval urbanism traced by UAV-lidar in highland Central Asia.

Aerial light detection and ranging (lidar) has emerged as a powerful technology for mapping urban archaeological landscapes, especially where dense vegetation obscures site visibility. More recently, uncrewed aerial vehicle/drone lidar scanning has markedly improved the resolution of three-dimensional point clouds, allowing for the detection of slight traces of structural features at centimetres of detail across large archaeological sites, a method particularly useful in areas such as mountains, where rapid deposition and erosion irregularly bury and expose archaeological remains. Here we present the results of uncrewed aerial vehicle-lidar surveys in Central Asia, conducted at two recently discovered archaeological sites in southeastern Uzbekistan: Tashbulak and Tugunbulak.

Archaeological and molecular evidence for ancient chickens in Central Asia.

The origins and dispersal of the chicken across the ancient world remains one of the most enigmatic questions regarding Eurasian domesticated animals. The lack of agreement concerning timing and centers of origin is due to issues with morphological identifications, a lack of direct dating, and poor preservation of thin, brittle bird bones. Here we show that chickens were widely raised across southern Central Asia from the fourth century BC through medieval periods, likely dispersing along the ancient Silk Road.

Charge transport in individual short base stacked single-stranded RNA molecules.

Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure the electrical conductance of particular 5-base and 10-base single-stranded (ss) RNA sequences capable of base stacking.

Biomechanics, Energetics, and Structural Basis of Rupture of Fibrin Networks.

Fibrin provides the main structural integrity and mechanical strength to blood clots. Failure of fibrin clots can result in life-threating complications, such as stroke or pulmonary embolism. The dependence of rupture resistance of fibrin networks (uncracked and cracked) on fibrin(ogen) concentrations in the (patho)physiological 1-5 g L range is explored by performing the ultrastructural studies and theoretical analysis of the experimental stress-strain profiles available from mechanical tensile loading assays.

Mechanical fatigue testing in silico: Dynamic evolution of material properties of nanoscale biological particles.

Biological particles have evolved to possess mechanical characteristics necessary to carry out their functions. We developed a computational approach to "fatigue testing in silico", in which constant-amplitude cyclic loading is applied to a particle to explore its mechanobiology. We used this approach to describe dynamic evolution of nanomaterial properties and low-cycle fatigue in the thin spherical encapsulin shell, thick spherical Cowpea Chlorotic Mottle Virus (CCMV) capsid, and thick cylindrical microtubule (MT) fragment over 20 cycles of deformation.

Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics.

Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs.

Paleolithic occupation of arid Central Asia in the Middle Pleistocene.

Central Asia is positioned at a crossroads linking several zones important to hominin dispersal during the Middle Pleistocene. However, the scarcity of stratified and dated archaeological material and paleoclimate records makes it difficult to understand dispersal and occupation dynamics during this time period, especially in arid zones. Here we compile and analyze paleoclimatic and archaeological data from Pleistocene Central Asia, including examination of a new layer-counted speleothem-based multiproxy record of hydrological changes in southern Uzbekistan at the end of MIS 11.

Morphotype broadening of the grapevine (Vitis vinifera L.) from Oxus civilization 4000 BP, Central Asia.

The region of Transoxiana underwent an early agricultural-demographic transition leading to the earliest proto-urban centers in Central Asia. The agronomic details of this cultural shift are still poorly studied, especially regarding the role that long-generation perennials, such as grapes, played in the cultivation system. In this paper, we present directly dated remains of grape pips from the early urban centers of Sapalli and Djarkutan, in south Uzbekistan.

Single-molecule conductance of double-stranded RNA oligonucleotides.

RNA oligonucleotides are crucial for a range of biological functions and in many biotechnological applications. Herein, we measured, for the first time, the conductance of individual double-stranded (ds)RNA molecules and compared it with the conductance of single DNA : RNA hybrids. The average conductance values are similar for both biomolecules, but the distribution of conductance values shows an order of magnitude higher variability for dsRNA, indicating higher molecular flexibility of dsRNA.

Strength, deformability and toughness of uncrosslinked fibrin fibers from theoretical reconstruction of stress-strain curves.

Structural mechanisms underlying the mechanical properties of fibrin fibers are elusive. We combined tensile testing of uncrosslinked fibrin polymers in vitro and in silico to explore their material properties. The experimental stress (σ) - strain (ε) curves for fibrin fibers are characterized by elastic deformations with a weaker elastic response for ε<160% due to unraveling of αC tethers and straightening of fibrin protofibrils, and a stronger response for ε>160% owing to unfolding of the coiled coils and γ nodules in fibrin monomers.

Strength and deformability of fibrin clots: Biomechanics, thermodynamics, and mechanisms of rupture.

Fibrin is the major determinant of the mechanical stability and integrity of blood clots and thrombi. To explore the rupture of blood clots, emulating thrombus breakage, we stretched fibrin gels with single-edge cracks of varying size. Ultrastructural alterations of the fibrin network correlated with three regimes of stress vs.

Statistical Learning from Single-Molecule Experiments: Support Vector Machines and Expectation-Maximization Approaches to Understanding Protein Unfolding Data.

Single-molecule force spectroscopy has become a powerful tool for the exploration of dynamic processes that involve proteins; yet, meaningful interpretation of the experimental data remains challenging. Owing to low signal-to-noise ratio, experimental force-extension spectra contain force signals due to nonspecific interactions, tip or substrate detachment, and protein desorption. Unravelling of complex protein structures results in the unfolding transitions of different types.

Fluctuating nonlinear spring theory: Strength, deformability, and toughness of biological nanoparticles from theoretical reconstruction of force-deformation spectra.

We developed the Fluctuating Nonlinear Spring (FNS) model to describe the dynamics of mechanical deformation of biological particles, such as virus capsids. The theory interprets the force-deformation spectra in terms of the "Hertzian stiffness" (non-linear regime of a particle's small-amplitude deformations), elastic constant (large-amplitude elastic deformations), and force range in which the particle's fracture occurs. The FNS theory enables one to quantify the particles' elasticity (Young's moduli for Hertzian and bending deformations), and the limits of their strength (critical forces, fracture toughness) and deformability (critical deformations) as well as the probability distributions of these properties, and to calculate the free energy changes for the particle's Hertzian, elastic, and plastic deformations, and eventual fracture.

Botulinum Endopeptidase: SAXS Experiments and MD Simulations Reveal Extended Solution Structures That Account for Its Biochemical Properties.

Development of antidotes against botulism requires understanding of the enzymatically active conformations of Botulinum neurotoxin serotype A (BoNT/A) light chain (LCA). We performed small angle X-ray scattering (SAXS) to characterize the solution structures of truncated light chain (tLCA). The 34-37 Å radius of gyration of tLCA was 1.

The formation of human populations in South and Central Asia.

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population.

Correction: Arboreal crops on the medieval Silk Road: Archaeobotanical studies at Tashbulak.

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

Arboreal crops on the medieval Silk Road: Archaeobotanical studies at Tashbulak.

During the first millennium A.D., Central Asia was marked by broad networks of exchange and interaction, what many historians collectively refer to as the "Silk Road".

Urban and nomadic isotopic niches reveal dietary connectivities along Central Asia's Silk Roads.

The ancient 'Silk Roads' formed a vast network of trade and exchange that facilitated the movement of commodities and agricultural products across medieval Central Asia via settled urban communities and mobile pastoralists. Considering food consumption patterns as an expression of socio-economic interaction, we analyse human remains for carbon and nitrogen isotopes in order to establish dietary intake, then model isotopic niches to characterize dietary diversity and infer connectivity among communities of urbanites and nomadic pastoralists. The combination of low isotopic variation visible within urban groups with isotopic distinction between urban communities irrespective of local environmental conditions strongly suggests localized food production systems provided primary subsistence rather than agricultural goods exchanged along trade routes.

TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid.

A new computational methodology for the accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and [Formula: see text]-based coarse-grained structural models of biological particles. The methodology mapped into the software package TensorCalculator was successfully applied to the empty cowpea chlorotic mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid.