Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure.

MicroRNAs (miRNAs) typically downregulate protein expression from target mRNAs through limited base-pairing interactions between the 5' 'seed' region of the miRNA and the mRNA 3' untranslated region (3'UTR). In contrast to this established mode of action, the liver-specific human miR-122 binds at two sites within the hepatitis C viral (HCV) 5'UTR, leading to increased production of infectious virions. We show here that two copies of miR-122 interact with the HCV 5'UTR at partially overlapping positions near the 5' end of the viral transcript to form a stable ternary complex. Both miR-122 binding sites involve extensive base pairing outside of the seed sequence; yet, they have substantially different interaction affinities. Structural probing reveals changes in the architecture of the HCV 5'UTR that occur on interaction with miR-122. In contrast to previous reports, however, results using both the recombinant cytoplasmic exonuclease Xrn1 and liver cell extracts show that miR-122-mediated protection of the HCV RNA from degradation does not correlate with stimulation of viral propagation in vivo. Thus, the miR-122:HCV ternary complex likely functions at other steps critical to the viral life cycle

Molecular techniques reveal cryptic life history and demographic processes of a critically endangered marine turtle

The concept of ‘effective population size’ (Ne), which quantifies how quickly a population will lose genetic variability, is one of the most important contributions of theoretical evolutionary biology to practical conservation management. Ne is often much lower than actual population size: how much so depends on key life history and demographic parameters, such as mating systems and population connectivity, that often remain unknown for species of conservation concern. Molecular techniques allow the indirect study of these parameters, as well as the estimation of current and historical Ne. Here, we use genotyping to assess the genetic health of an important population of the critically endangered hawksbill turtle (Eretmochelys imbricata), a slow-to-mature, difficult-to-observe species with a long history of severe overhunting. Our results were surprisingly positive: we found that the study population, located in the Republic of Seychelles, Indian Ocean, has a relatively large Ne, estimated to exceed 1000, and showed no evidence of a recent reduction in Ne (i.e. no genetic bottleneck). Furthermore, molecular inferences suggest the species' mating system is conducive to maintaining a large Ne, with a relatively large and widely distributed male population promoting considerable gene flow amongst nesting sites across the Seychelles area. This may also be reinforced by the movement of females between nesting sites. Our study underlines how molecular techniques can help to inform conservation biology. In this case our results suggest that this important hawksbill population is starting from a relatively strong position as it faces new challenges, such as global climate change

Improved weed management for transplanted aman rice

Rainfed transplanted rice grown in the monsoon aman season accounts for more than 50% of the total area planted to rice in Bangladesh. Because of rising input costs, including labor, farmers are searching for ways to maintain income, by either increasing yields or reducing costs or both. On-farm trials in the High Barind Tract indicated that one-third of the farmers would be able to gain 0.5 t ha–1 or more additional grain by undertaking more intensive or timelier weeding than is usual under current management practices. Higher yields were observed on-farm from a preemergence application of butachlor(1.25 kg a.i. ha–1) compared with hand weeding twice. In Comilla District, trials of a range of weed management practices demonstrated that the yield advantage over the farmers’ practice, either one or two hand weedings, was on average 355 ± 18 kg ha–1 for Rifit (pretilachlor), 281 ± 39 kg ha–1 for Machete (butachlor), and 210 ± 34 kg ha–1 for Ronstar (oxadiazon), each followed by one hand weeding in aman 2003. Partial budgets calculated for inputs and returns showed that hand weeding was less profitable than herbicides in rainfed rice,incurring US$72 ha–1 lower return. Use of a push weeder plus one hand weeding was less profitable than herbicides, incurring$49 ha–1 lower return. To date, herbicides have been largely promoted for irrigated rice in Bangladesh. The trial results demonstrate that under rainfed conditions early in the aman season, water levels are adequate for herbicides to work effectively. The use of herbicides allows timely weed control when there is a shortage of labor and avoids transaction costs, such as the provision of meals and time needed to source laborers. Herbicides are likely to be adopted by growers experiencing labor shortages, particularly on large farms and for farmers seeking to reduce input costs. Sharecroppers and tenant farmers who pay rent are primarily concerned about obtaining a high aman yield, so innovations that raise aman yields (such as herbicides that will have a similar effect as a timely first weeding) are also likely to be adopted on sharecropped plots, even when costs are not shared between the landlord and tenant

Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation.

The initiation of protein synthesis plays an essential regulatory role in human biology. At the center of the initiation pathway, the 13-subunit eukaryotic translation initiation factor 3 (eIF3) controls access of other initiation factors and mRNA to the ribosome by unknown mechanisms. Using electron microscopy (EM), bioinformatics and biochemical experiments, we identify two highly conserved RNA-binding motifs in eIF3 that direct translation initiation from the hepatitis C virus internal ribosome entry site (HCV IRES) RNA. Mutations in the RNA-binding motif of subunit eIF3a weaken eIF3 binding to the HCV IRES and the 40S ribosomal subunit, thereby suppressing eIF2-dependent recognition of the start codon. Mutations in the eIF3c RNA-binding motif also reduce 40S ribosomal subunit binding to eIF3, and inhibit eIF5B-dependent steps downstream of start codon recognition. These results provide the first connection between the structure of the central translation initiation factor eIF3 and recognition of the HCV genomic RNA start codon, molecular interactions that likely extend to the human transcriptome

Hydrodynamic propulsion of human sperm

The detailed fluid mechanics of sperm propulsion are fundamental to our understanding of reproduction. In this paper, we aim to model a human sperm swimming in a microscope slide chamber. We model the sperm itself by a distribution of regularized stokeslets over an ellipsoidal sperm head and along an infinitesimally thin flagellum. The slide chamber walls are modelled as parallel plates, also discretized by a distribution of regularized stokeslets. The sperm flagellar motion, used in our model, is obtained by digital microscopy of human sperm swimming in slide chambers. We compare the results of our simulation with previous numerical studies of flagellar propulsion, and compare our computations of sperm kinematics with those of the actual sperm measured by digital microscopy. We find that there is an excellent quantitative match of transverse and angular velocities between our simulations and experimental measurements of sperm. We also find a good qualitative match of longitudinal velocities and computed tracks with those measured in our experiment. Our computations of average sperm power consumption fall within the range obtained by other authors. We use the hydrodynamic model, and a prototype flagellar motion derived from experiment, as a predictive tool, and investigate how sperm kinematics are affected by changes to head morphology, as human sperm have large variability in head size and shape. Results are shown which indicate the increase in predicted straight-line velocity of the sperm as the head width is reduced and the increase in lateral movement as the head length is reduced. Predicted power consumption, however, shows a minimum close to the normal head aspect ratio

The initiation and development of metamorphic foliation in the Otago Schist, Part 2: evidence from quartz grain-shape data

Shape, size and orientation measurements of quartz grains sampled along two transects that cross zones of increasing metamorphic grade in the Otago Schist, New Zealand, reveal the role of quartz in the progressive development of metamorphic foliation. Sedimentary compaction and diagenesis contributed little to the formation of a shape-preferred orientation (SPO) within the analysed samples. Metamorphic foliation was initiated at sub-greenschist facies conditions as part of a composite S1-bedding structure parallel to the axial planes of tight to isoclinal F1 folds. An important component of this foliation is a pronounced quartz SPO that formed dominantly by the effect of dissolution?precipitation creep on detrital grains in association with F1 strain. With increasing grade, the following trends are evident from the SPO data: (i) a progressive increase in the aspect ratio of grains in sections parallel to lineation, and the development of blade-shaped grains; (ii) the early development of a strong shape preferred orientation so that blade lengths define the linear aspect of the foliation (lineation) and the intermediate axes of the blades define a partial girdle about the lineation; (iii) a slight thinning and reduction in volume of grains in the one transect; and (iv) an actual increase in thickness and volume in the survivor grains of the second transect. The highest-grade samples, within the chlorite zone of the greenschist facies, record segregation into quartz- and mica-rich layers. This segregation resulted largely from F2 crenulation and marks a key change in the distribution, deformation and SPO of the quartz grains. The contribution of quartz SPO to defining the foliation lessens as the previously discrete and aligned detrital quartz grains are replaced by aggregates and layers of dynamically recrystallized quartz grains of reduced aspect ratio and reduced alignment. Pressure solution now affects the margins of quartz-rich layers rather than individual grains. In higher-grade samples, therefore, the rock structure is characterized increasingly by segregation layering parallel to a foliation defined predominantly by mica SPO