Phylogenetic and coalescent analysis of three loci suggest that the Water Rail is divisible into two species, Rallus aquaticus and R. indicus

<p>Abstract</p> <p>Background</p> <p>Water Rails (<it>Rallus aquaticus</it>) inhabit fragmented freshwater wetlands across their Palearctic distribution. Disjunct populations are now thought to be morphologically similar over their vast geographic range, though four subspecies had been recognized previously. The fossil record suggests that Water Rails (<it>R. aquaticus</it>) were already spread across the Palearctic by the Pleistocene ~2 million years ago, and the oldest fossil remains thought to be closely related to the common ancestor of water rails date from the Pliocene.</p> <p>Results</p> <p>To investigate population structure in Water Rails at the genetic level we sequenced three independent loci: 686 base pairs (bp) of the mitochondrial DNA <it>COI </it>barcode; 618 bp of the intron <it>ADH5</it>; and 746 bp of the exon <it>PTPN12</it>. Phylogeographic analysis revealed that Water Rails breeding in eastern Asia (<it>R. a. indicus</it>, also known as the Brown-cheeked Rail) are strongly differentiated from the Water Rails in Western and Middle Asia and Europe (<it>R. a. aquaticus </it>and <it>R. a. korejewi</it>). The Kimura 3-parameter plus Gamma <it>COI </it>genetic distance between these two geographic groups was > 3%, and they differed by 18 diagnostic substitutions commensurate with differences between recently diverged sister species of birds. In spite of the low number of variable sites, the two nuclear loci supported this split. We estimated the split of the Brown-cheeked Rail and the Water Rail to have occurred ~534,000 years ago (95% CI 275,000-990,000 years ago). Fragmentation of the widespread ancestral population and eventual speciation of water rails is likely attributable to vicariance by a barrier formed by glacial cycles, continuous uplift of the Tibetan Plateau and increased sedimentation in deserts in southern Asia that originated in the Miocene.</p> <p>Conclusions</p> <p>Water Rails from East Asia were genetically differentiated from the ones breeding in Europe and Western to Middle Asia. Most of the genetic signal was from mitochondrial <it>COI</it>, and was corroborated by polymorphic sites in the two nuclear loci we employed. The split between these two lineages was estimated to occur in the Middle Pleistocene, when populations were isolated in disjunct wetlands with little or no gene flow. Independent evidence from differences in morphology and vocalizations in concert with genetic differentiation and a long history of isolation support recognition of the Brown-cheeked Rail breeding in East Asia as a separate species, <it>R. indicus</it>. The use of several independent loci is invaluable in inferring species trees from gene trees and in recognizing species limits.</p

Divergent evolution of protein conformational dynamics in dihydrofolate reductase.

Molecular evolution is driven by mutations, which may affect the fitness of an organism and are then subject to natural selection or genetic drift. Analysis of primary protein sequences and tertiary structures has yielded valuable insights into the evolution of protein function, but little is known about the evolution of functional mechanisms, protein dynamics and conformational plasticity essential for activity. We characterized the atomic-level motions across divergent members of the dihydrofolate reductase (DHFR) family. Despite structural similarity, Escherichia coli and human DHFRs use different dynamic mechanisms to perform the same function, and human DHFR cannot complement DHFR-deficient E. coli cells. Identification of the primary-sequence determinants of flexibility in DHFRs from several species allowed us to propose a likely scenario for the evolution of functionally important DHFR dynamics following a pattern of divergent evolution that is tuned by cellular environment

Conformational dynamics of a membrane protein chaperone enables spatially regulated substrate capture and release

Membrane protein biogenesis poses enormous challenges to cellular protein homeostasis and requires effective molecular chaperones. Compared with chaperones that promote soluble protein folding, membrane protein chaperones require tight spatiotemporal coordination of their substrate binding and release cycles. Here we define the chaperone cycle for cpSRP43, which protects the largest family of membrane proteins, the light harvesting chlorophyll a/b-binding proteins (LHCPs), during their delivery. Biochemical and NMR analyses demonstrate that cpSRP43 samples three distinct conformations. The stromal factor cpSRP54 drives cpSRP43 to the active state, allowing it to tightly bind substrate in the aqueous compartment. Bidentate interactions with the Alb3 translocase drive cpSRP43 to a partially inactive state, triggering selective release of LHCP’s transmembrane domains in a productive unloading complex at the membrane. Our work demonstrates how the intrinsic conformational dynamics of a chaperone enables spatially coordinated substrate capture and release, which may be general to other ATP-independent chaperone systems

A Disorder-to-Order Transition Activates an ATP-Independent Membrane Protein Chaperone

The 43 kDa subunit of the chloroplast signal recognition particle, cpSRP43, is an ATP-independent chaperone essential for the biogenesis of the light harvesting chlorophyll-binding proteins (LHCP), the most abundant membrane protein family on earth. cpSRP43 is activated by a stromal factor, cpSRP54, to more effectively capture and solubilize LHCPs. The molecular mechanism underlying this chaperone activation is unclear. Here, a combination of hydrogen–deuterium exchange, electron paramagnetic resonance, and NMR spectroscopy experiments reveal that a disorder-to-order transition of the ankyrin repeat motifs in the substrate binding domain of cpSRP43 drives its activation. An analogous coil-to-helix transition in the bridging helix, which connects the ankyrin repeat motifs to the cpSRP54 binding site in the second chromodomain, mediates long-range allosteric communication of cpSRP43 with its activating binding partner. Our results provide a molecular model to explain how the conformational dynamics of cpSRP43 enables regulation of its chaperone activity and suggest a general mechanism by which ATP-independent chaperones with cooperatively folding domains can be regulated

Dynamic prediction model to identify young children at high risk of future overweight: Development and internal validation in a cohort study

Background: Primary prevention of overweight is to be preferred above secondary prevention, which has shown moderate effectiveness. Objective: To develop and internally validate a dynamic prediction model to identify young children in the general population, applicable at every age between birth and age 6, at high risk of future overweight (age 8). Methods: Data were used from the Prevention and Incidence of Asthma and Mite Allergy birth cohort, born in 1996 to 1997, in the Netherlands. Participants for whom data on the outcome overweight at age 8 and at least three body mass index SD scores (BMI SDS) at the age of ≥3 months and ≤6 years were available, were included (N = 2265). The outcome of the prediction model is overweight (yes/no) at age 8 (range 7.4-10.5 years), defined according to the sex- and age-specific BMI cut-offs of the International Obesity Task Force. Results: After backward selection in a Generalized Estimating Equations analysis, the prediction model included the baseline predictors maternal BMI, paternal BMI, paternal education, birthweight, sex, ethnicity and indoor smoke exposure; and the longitudinal predictors BMI SDS, and the linear and quadratic terms of the growth curve describing a child's BMI SDS development over time, as well as the longitudinal predictors' interactions with age. The area under the curve of the model after internal validation was 0.845 and Nagelkerke R2 was 0.351. Conclusions: A dynamic prediction model for overweight was developed with a good predictive ability using easily obtainable predictor information. External validation is needed to confirm that the model has potential for use in practice

Limited Value of Staging Squamous Cell Carcinoma of the Anal Margin and Canal Using the Sentinel Lymph Node Procedure: A Prospective Study with Long-Term Follow-Up

Background. Selection of patients with anal cancer for groin irradiation is based on tumor size, palpation, ultrasound, and fine needle cytology. Current staging of anal cancer may result in undertreatment in small tumors and overtreatment of large tumors. This study reports the feasibility of the sentinel lymph node biopsy (SLNB) in patients with anal cancer and whether this improves the selection for inguinal radiotherapy. Methods. A total of 50 patients with squamous anal cancer were evaluated prospectively. Patients without a SLNB (n = 29) received irradiation of the inguinal lymph nodes based on lymph node status, tumor size, and location of the primary tumor. Inguinal irradiation treatment in patients with a SLNB was based on the presence of metastases in the SLN. Results. SLNs were found in all 21 patients who underwent a SLNB. There were 5 patients (24%) who had complications after SLNB and 7 patients (33%) who had a positive SLN and received inguinal irradiation. However, 2 patients with a tumor-free SLN and no inguinal irradiation developed lymph node metastases after 12 and 24 months, respectively. Conclusions. We conclude that SLNB in anal cancer is technically feasible. SLNB can identify those patients who would benefit from refrain of inguinal irradiation treatment and thereby reducing the incidence of unnecessary inguinal radiotherapy. However, because of the occurrence of inguinal lymph node metastases after a tumor-negative SLNB, introduction of this procedure as standard of care in all patients with anal carcinoma should be done with caution to avoid undertreatment of patient who otherwise would benefit from inguinal radiotherapy