BKV Agnoprotein Interacts with α-Soluble N-Ethylmaleimide-Sensitive Fusion Attachment Protein, and Negatively Influences Transport of VSVG-EGFP

Background: The human polyomavirus BK (BKV) infects humans worldwide and establishes a persistent infection in the kidney. The BK virus genome encodes three regulatory proteins, large and small tumor-antigen and the agnoprotein, as well as the capsid proteins VP1 to VP3. Agnoprotein is conserved among BKV, JC virus (JCV) and SV40, and agnoprotein-deficient mutants reveal reduced viral propagation. Studies with JCV and SV40 indicate that their agnoproteins may be involved in transcription, replication and/or nuclear and cellular release of the virus. However, the exact function(s) of agnoprotein of BK virus remains elusive. Principal Findings: As a strategy of exploring the functions of BKV agnoprotein, we decided to look for cellular interaction partners for the viral protein. Several partners were identified by yeast two-hybrid assay, among them a-SNAP which is involved in disassembly of vesicles during secretion. BKV agnoprotein and a-SNAP were found to partially co-localize in cells, and a complex consisting of agnoprotein and a-SNAP could be co-immunoprecipitated from cells ectopically expressing the proteins as well as from BKV-transfected cells. The N-terminal part of the agnoprotein was sufficient for the interaction with a-SNAP. Finally, we could show that BKV agnoprotein negatively interferes with secretion of VSVG-EGFP reporter suggesting that agnoprotein may modulate exocytosis. Conclusions: We have identified the first cellular interaction partner for BKV agnoprotein. The most N-terminal part of BKV agnoprotein is involved in the interaction with a-SNAP. Presence of BKV agnoprotein negatively interferes with secretion of VSVG-EGFP reporter

Plio-Pleistocene climatic change had a major impact on the assembly and disassembly processes of Iberian rodent communities

Comprehension of changes in community composition through multiple spatio-temporal scales is a prime challenge in ecology and palaeobiology. However, assembly, structuring and disassembly of biotic metacommunities in deep-time is insufficiently known. To address this, we used the extensively sampled Iberian Plio-Pleistocene fossil record of rodent faunas as our model system to explore how global climatic events may alter metacommunity structure. Through factor analysis, we found five sets of genera, called faunal components, which co-vary in proportional diversity over time. These faunal components had different spatio-temporal distributions throughout the Plio-Pleistocene, resulting in non-random changes in species assemblages, particularly in response to the development of the Pleistocene glaciations. Three successive metacommunities with distinctive taxonomic structures were identified as a consequence of the differential responses of their members to global climatic change: (1) Ruscinian subtropical faunas (5.3–3.4 Ma) dominated by a faunal component that can be considered as a Miocene legacy; (2) transition faunas during the Villafranchian–Biharian (3.4–0.8 Ma) with a mixture of different faunal components; and (3) final dominance of the temperate Toringian faunas (0.8–0.01 Ma) that would lead to the modern Iberian assemblage. The influence of the cooling global temperature drove the reorganisation of these rodent metacommunities. Selective extinction processes due to this large-scale environmental disturbance progressively eliminated the subtropical specialist species from the early Pliocene metacommunity. This disassembly process was accompanied by the organisation of a diversified metacommunity with an increased importance of biome generalist species, and finally followed by the assembly during the middle–late Pleistocene of a new set of species specialised in the novel environments developed as a consequence of the glaciations

BioTIME 2.0: Expanding and Improving a Database of Biodiversity Time Series

Motivation Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database. Main Types of Variables Included The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years. Spatial Location and Grain Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size. Time Period and Grain The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric. Major Taxa and Level of Measurement The database includes any eukaryotic taxa, with a combined total of 56,400 taxa. Software Format csv and. SQL

Growth plate senescence is more advanced in shorter bones than in longer bones.

(A) Masson Trichrome–stained histological sections of proximal tibias, distal femurs, distal metacarpals, and proximal forelimb phalanges from C57BL/6 mice at various ages. Cartilage matrix stains light blue; bone matrix, dark blue. Epiphyseal fusion (disappearance of growth plate) occurs at approximately 3 weeks in phalanges and 4 weeks in metacarpals but has not yet occurred at 12 weeks in tibias or femurs. Scale bar, 100 μm. (B–G) Quantitative histological measurements of RZ height (panel B) and cell count (panel C), PZ height (panel D) and cell count per column (panel E), HZ height (panel F) and cell count per column (panel G), in each of the 4 growth plates at various ages. N = 6, mean ± SEM. Raw values for Fig 2B–2G are available in S1 Data. HZ, hypertrophic zone; PZ, proliferative zone; RZ, resting zone.</p

Differential aging of growth plate cartilage underlies differences in bone length and thus helps determine skeletal proportions

<div><p>Bones at different anatomical locations vary dramatically in size. For example, human femurs are 20-fold longer than the phalanges in the fingers and toes. The mechanisms responsible for these size differences are poorly understood. Bone elongation occurs at the growth plates and advances rapidly in early life but then progressively slows due to a developmental program termed “growth plate senescence.” This developmental program includes declines in cell proliferation and hypertrophy, depletion of cells in all growth plate zones, and extensive underlying changes in the expression of growth-regulating genes. Here, we show evidence that these functional, structural, and molecular senescent changes occur earlier in the growth plates of smaller bones (metacarpals, phalanges) than in the growth plates of larger bones (femurs, tibias) and that this differential aging contributes to the disparities in bone length. We also show evidence that the molecular mechanisms that underlie the differential aging between different bones involve modulation of critical paracrine regulatory pathways, including insulin-like growth factor (Igf), bone morphogenetic protein (Bmp), and Wingless and Int-1 (Wnt) signaling. Taken together, the findings reveal that the striking disparities in the lengths of different bones, which characterize normal mammalian skeletal proportions, is achieved in part by modulating the progression of growth plate senescence.</p></div

Disparities in chondrocyte proliferation, chondrocyte hypertrophy, and bone growth rate between shorter and longer bones.

<p>(A) Fluorescent images of proximal tibias, distal femurs, distal metacarpals, and proximal forelimb phalanges from mice at various postnatal ages. Rate of longitudinal bone growth was determined from the distance (vertical red bars) between the chondro-osseous junction (white dotted line) and the calcein-labeled (fluorescent green) bone. DAPI was used for counterstain. Scale bar, 200 μm. (B) Masson Trichrome–stained histological sections of hypertrophic zone of proximal tibias, distal femurs, distal metacarpals, and proximal forelimb phalanges, from C57BL/6 mice at E17.5 and various postnatal ages. Hypertrophic cell height diminished earlier in the metacarpals and phalanges. Scale bar, 30 μm. (C) Quantitative histological measurements of TH cell height (upper panel) and number of BrdU-labeled cells per column in the proliferative zone (middle panel), and rate of bone growth measured by calcein-labeling (lower panel). (D) Position-specific BrdU labeling indices of proliferative zone of proximal tibias, distal femurs, distal metacarpals, and proximal forelimb phalanges in 1- and 4-week-old mice. Cell position 1 denotes the proliferative chondrocyte closest to the resting zone, and black arrow indicates the cell position where the proliferative zone ends and the pre-hypertrophic region starts. Position-specific BrdU labeling indices at other time points are depicted in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2005263#pbio.2005263.s004" target="_blank">S4 Fig</a>. Raw values for Fig 1C and 1D are available in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2005263#pbio.2005263.s020" target="_blank">S1 Data</a>. BrdU, 5-bromo-2-deoxyuridine; E17.5, embryonic day 17.5; TH, terminal hypertrophic.</p

Differences in bone length arise in part from modulation of the developmental program of growth plate senescence.

<p>(A) Senescent changes in gene expression in the growth plate, including genes encoding many paracrine signaling molecules, are more advanced in the shorter bones. (B) Age-independent differences in gene expression within key regulatory pathways also contribute to differences in growth rate. (C) Consequently, the developmental program of growth plate senescence, including structural involution and declines in proliferation and hypertrophic cell size, is more advanced in shorter bones. (D) Differences in proliferation rate and hypertrophic cell size result in disparities in the rate of bone elongation and thus cumulative bone length. Bmp, bone morphogenetic protein; GP, growth plate; IGF, insulin-like growth factor; Igfbp, IGF-binding protein; Wif, Wnt inhibitory factor; Wnt, Wingless and Int-1.</p

Differences in specific paracrine signaling pathways contribute to disparities in growth plate function between different bones.

<p>RNA-Seq was used to identify genes differentially expressed between proximal tibia and proximal phalanx (>2-fold, FDR < 0.05, both species, age 1 week). (A) Gene ontology and signaling pathway analyses showed enrichment for developmental-related functions and identified pathways previously implicated in growth plate biology. (B, C) Heatmaps were generated by hierarchical clustering of the 150 genes that showed the greatest differential expression between tibia and phalanx. Scale bar represents log₂ (fold differences). (D–F) Specific genes from IGF (panel D), BMP (panel E), and Wnt (panel F) signaling pathways that showed significant differential expression between 1-week tibia and phalanx by RNA-Seq were selected for validation by qPCR and to determine time course. (G, H) When cultured in monolayer, primary mouse chondrocytes isolated from tibias showed higher Igf2 expression (panel G, light green bars) and more rapid proliferation (panel H, open light green bars) than those from phalanges. Proliferation of phalangeal chondrocytes, but not tibial chondrocytes, responded positively to exogenous Igf1 (panel H, striped light green bars). When treated with siRNA against Igf2 (no exogenous Igf1; panel G, dark green bars), proliferation was inhibited (versus control) in tibial chondrocytes but not phalangeal chondrocytes (panel H, open dark green bars). This inhibition was partially reversed by exogenous Igf1 (panel H, striped dark green bar). (I) Western blot showed higher levels of p-SMAD1/5/9 in tibial/femoral growth plate chondrocytes than metacarpal/phalangeal chondrocytes, implying more active BMP signaling in the longer bones. (J, K) Neonatal mouse tibias and metatarsals were treated with Bmp2 or Noggin in culture for 3 days, followed by histological examination for chondrocyte hypertrophy. Scale bar, 50 μm. <i>N</i> = 8–10; horizontal line represents sample means. Raw values for Fig 4D–4H, and K are available in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2005263#pbio.2005263.s020" target="_blank">S1 Data</a>. BMP, bone morphogenetic protein; FDR, false discovery rate; IGF, insulin-like growth factor; pSMAD1/5/9, phosphorylated SMAD1/5/9; qPCR, quantitative PCR; RNA-Seq, RNA sequencing; siRNA, small interfering RNA; Wnt, Wingless and Int-1.</p