A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses

Simian Foamy Virus (SFV) can be transmitted from non-human primates (NHP) to humans. However, there are no documented cases of human to human transmission, and significant differences exist between infection in NHP and human hosts. The mechanism for these between-host differences is not completely understood. In this paper we develop a new Bayesian approach to the detection of APOBEC3-mediated hypermutation, and use it to compare SFV sequences from human and NHP hosts living in close proximity in Bangladesh. We find that human APOBEC3G can induce genetic changes that may prevent SFV replication in infected humans in vivo.     

The role of Wnt/β‐catenin signaling in proliferation and regeneration of the developing basilar papilla and lateral line

Canonical Wnt/β‐catenin signaling has been implicated in multiple developmental events including the regulation of proliferation, cell fate, and differentiation. In the inner ear, Wnt/β‐catenin signaling is required from the earliest stages of otic placode specification through the formation of the mature cochlea. Within the avian inner ear, the basilar papilla (BP), many Wnt pathway components are expressed throughout development. Here, using reporter constructs for Wnt/β‐catenin signaling, we show that this pathway is active throughout the BP (E6‐E14) in both hair cells (HCs) and supporting cells. To characterize the role of Wnt/β‐catenin activity in developing HCs, we performed gain‐ and loss‐of‐function experiments in vitro and in vivo in the chick BP and zebrafish lateral line systems, respectively. Pharmacological inhibition of Wnt signaling in the BP and lateral line neuromasts during the periods of proliferation and HC differentiation resulted in reduced proliferation and decreased HC formation. Conversely, pharmacological activation of this pathway significantly increased the number of HCs in the lateral line and BP. Results demonstrated that this increase was the result of up‐regulated cell proliferation within the Sox2‐positive cells of the prosensory domains. Furthermore, Wnt/β‐catenin activation resulted in enhanced HC regeneration in the zebrafish lateral line following aminoglycoside‐induced HC loss. Combined, our data suggest that Wnt/β‐catenin signaling specifies the number of cells within the prosensory domain and subsequently the number of HCs. This ability to induce proliferation suggests that the modulation of Wnt/β‐catenin signaling could play an important role in therapeutic HC regeneration. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 74: 438–456, 2014     

Variable reproductive success in fragmented populations

Marine habitats are naturally patchy and anthropogenic disturbance can further fragment them. Many marine animals are sessile as adults or obligate inhabitants of particular habitats, so populations living in isolated patches of habitat are linked largely by dispersal of planktonic larvae. Theoretically, larvae are more likely to find and settle into large patches of habitat than small patches, thus small habitat patches may experience a more discontinuous supply of recruits resulting in small populations with unusual size- or age-structures or odd sex ratios — conditions where Allee effects on reproductive success are likely. We tested this hypothesis for the Caribbean spotted spiny lobster (Panulirus guttatus), an obligate inhabitant of coral patch reefs whose mating dynamics are size-dependent. We found that P. guttatus were less abundant on small reefs where their size structure and per capita reproductive success were significantly more variable, particularly among large females that are susceptible to sperm limitation that diminishes fertilization rates. These results are indicative of Allee effects and provide a mechanistic understanding of how size-dependent mating dynamics influence reproductive success in ways that alter population dynamics in patchy habitats.     

Functional Interaction between the Fanconi Anemia D2 Protein and Proliferating Cell Nuclear Antigen (PCNA) via a Conserved Putative PCNA Interaction Motif

Fanconi Anemia (FA) is a rare recessive disease characterized by congenital abnormalities, bone marrow failure, and cancer susceptibility. The FA proteins and the familial breast cancer susceptibility gene products, BRCA1 and FANCD1/BRCA2, function cooperatively in the FA-BRCA pathway to repair damaged DNA and to prevent cellular transformation. Activation of this pathway occurs via the mono-ubiquitination of the FANCD2 protein, targeting it to nuclear foci where it co-localizes with FANCD1/BRCA2, RAD51, and PCNA. The regulation of the mono-ubiquitination of FANCD2, as well as its function in DNA repair remain poorly understood. In this study, we have further characterized the interaction between the FANCD2 and PCNA proteins. We have identified a highly conserved, putative FANCD2 PCNA interaction motif (PIP-box), and demonstrate that mutation of this motif disrupts FANCD2-PCNA binding and precludes the mono-ubiquitination of FANCD2. Consequently, the FANCD2 PIP-box mutant protein fails to correct the mitomycin C hypersensitivity of FA-D2 patient cells. Our results suggest that PCNA may function as a molecular platform to facilitate the mono-ubiquitination of FANCD2 and activation of the FA-BRCA pathway.Fanconi anemia (FA)² is a rare recessive disorder characterized by developmental abnormalities, progressive bone marrow failure, and pronounced cancer susceptibility (1). FA patients are particularly susceptible to early-onset acute myelogenous leukemia and squamous cell carcinoma of the head, neck, and gynecologic regions (2). FA patient cells are hypersensitive to the clastogenic effects of DNA cross-linking agents, e.g. mitomycin C (MMC), and agents that inhibit DNA replication, e.g. aphidicolin (APH) (3, 4). There are currently thirteen genetically defined FA complementation groups (A, B, C, D1, D2, E, F, G, I, J, L, M, and N), and all thirteen genes have been identified (5).A central step in the activation of the FA-BRCA pathway is the mono-ubiquitination of the FANCD2 and FANCI proteins, catalyzed by the core FA E2/E3 holoenzyme complex (5, 6). The mono-ubiquitination of FANCD2 and FANCI signals their translocation to discrete nuclear foci, where they co-localize with the BRCA1 and RAD51 DNA repair proteins, as well as the major cellular DNA polymerase processivity factor PCNA (3, 4, 7–9). Several studies have suggested an important role for the FA-BRCA pathway in a DNA replication-associated DNA repair process, e.g. homologous recombination (HR), and/or translesion DNA synthesis (TLS) (3, 4, 10–12). Accordingly, additional proteins with established roles in the DNA replication stress response, including ATR, CHK1, HCLK2, and RPA, modulate DNA damage-inducible FANCD2 mono-ubiquitination (13–15). Our understanding of the regulation of this critical post-translational modification, however, is incomplete.We, and others (4, 7) have previously reported an association between FANCD2 and PCNA. FANCD2 and PCNA co-localize in nuclear foci following treatment with agents that inhibit DNA replication. Like FANCD2, PCNA is mono-ubiquitinated following exposure to DNA-damaging agents (16, 17). While FANCD2 and PCNA are mono-ubiquitinated by different E3 ubiquitin ligases, FANCL and RAD18 (16–19), respectively, both proteins are de-ubiquitinated by the USP1 enzyme (20, 21). The functional significance of the FANCD2-PCNA interaction, however, has not been determined.In addition to its role as a DNA polymerase processivity factor, PCNA interacts with many DNA repair proteins, e.g. MSH3, XPG, and p21^Cip1/Waf1 (22). These interactions typically occur in a hydrophobic pocket of the PCNA homotrimer, termed the interdomain connecting loop (ICL). Proteins that interact with the PCNA ICL harbor a highly conserved PCNA-binding motif called the PIP-box, defined by the amino acid sequence QXXhXXaa, where h represents amino acids with moderately hydrophobic side chains, e.g. leucine, isoleucine, or methionine (L, I, M), a represents amino acids with highly hydrophobic, aromatic side chains, e.g. phenylalanine and tyrosine (F, Y), and X is any amino acid (23).Here, we describe an important functional interaction between FANCD2 and PCNA. We have identified a highly conserved putative PIP-box in FANCD2, and demonstrate that mutation of this motif disrupts the FANCD2-PCNA interaction, and precludes both the spontaneous and DNA damage-inducible mono-ubiquitination of FANCD2. Consequently, the FANCD2 PIP-box mutant fails to correct the MMC hypersensitivity of FA-D2 patient-derived cells. However, the mutant protein retains the ability to localize to chromatin, interact with FANCE, and undergo DNA damage-inducible phosphorylation. Our results suggest that PCNA may act as a molecular platform for the mono-ubiquitination of FANCD2 and for the activation of the FA-BRCA pathway.     

COMPARISON OF THE SENSORY PROPERTIES OF ULTRA-HIGH-TEMPERATURE (UHT) MILK FROM DIFFERENT COUNTRIES

Shelf-stable milk, also known as ultra-high-temperature (UHT) milk is the most common form of milk in many parts of the world. This study compared the differences in flavor and texture of 37 commercially available UHT and sterilized milk samples including whole, 2% reduced-fat and low-fat milk obtained from markets in seven countries: France ( n =  2), Italy ( n =  11), Japan ( n =  1), Korea ( n =  2), Peru ( n =  3), Thailand ( n =  13) and the U.S.A. ( n =  5). Five highly trained panelists used flavor and texture profiling to describe the sensory properties of each milk sample. Data were analyzed by principal component analysis and hierarchical cluster analysis. Higher levels of processed, chalky, brown and cooked flavor notes generally corresponded to lower levels of fresh dairy flavor characteristics. In general, samples did not vary consistently within a country. Fat content did not correlate with dairy fat flavor or with viscosity. This research suggests that companies' manufacturing processes for UHT milk may have more impact than country or fat content in determining sensory properties of UHT milk.

PRACTICAL APPLICATIONS

Sensory properties of UHT milk from different countries developed in this study could be used by the dairy industry to understand the similarities and differences of UHT milk characteristics from different regions and to modify UHT milk characteristics to meet consumers' criteria or expectation. The study suggests that manufacturers who want to improve quality of UHT milk by modify flavor and texture properties should focus on improvements to the manufacturing processes.     

Engines of change: Transposable element mutation rates are high and variable within Daphnia magna

Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10⁻⁵ per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome.     

Giant,accordioned sperm acrosomes of the greater bulldog bat,Noctilio leporinus

Sperm of the greater bulldog bat Noctilio leporinus display an architecture that is totally unique among mammalian spermatozoa. The sperm head of Noctilio is extraordinarily large and flat and lies eccentrically with respect to the sperm tail. The major portion of the atypically large acrosome lies anterior to the nucleus and is shaped into a dozen accordionlike folds that run parallel to the long axis of the sperm. The ridge of each fold is shaped into ∼60 minute, evenly spaced rises that extend along the entire length of the fold. We speculate that acrosome ridges may serve to strengthen the sperm head during transport. Mol. Reprod. Dev. 48:90–94, 1997 © 1997 Wiley-Liss, Inc.     

Fecundity and size in the housefly: investigations of some environmental sources and genetic correlates of variation

Environmental sources and genetic correlates of variation in fecundity and size were studied in field and laboratory housefly populations in central Iowa, U.S.A. Electrophoresis of enzymatic proteins was used to monitor genotypes and heterozygosity. In the field, mean fecundity declined as adult densities increased. Fecundity varied greatly within breeding seasons. Fly body size varied spatially and temporally during summer and winter. Fecundity and size were positively correlated. Size was independent of genotypes at the six loci studied. No relationship was observed between heterozygosity and the magnitude or variability of body size.