Structure of monoubiquitinated PCNA

Ubiquitination of proliferating cell nuclear antigen (PCNA) to ub-PCNA is essential for DNA replication across bulky template lesions caused by UV radiation and alkylating agents, as ub-PCNA orchestrates the recruitment and switching of translesion synthesis (TLS) polymerases with replication polymerases. This allows replication to proceed, leaving the DNA to be repaired subsequently. Defects in a TLS polymerase, Pol η, lead to a form of Xeroderma pigmentosum, a disease characterized by severe skin sensitivity to sunlight damage and an increased incidence of skin cancer. Structurally, however, information on how ub-PCNA orchestrates the switching of these two classes of polymerases is lacking. We have solved the structure of ub-PCNA and demonstrate that the ubiquitin molecules in ub-PCNA are radially extended away from the PCNA without structural contact aside from the isopeptide bond linkage. This unique orientation provides an open platform for the recruitment of TLS polymerases through ubiquitin-interacting domains. However, the ubiquitin moieties, to the side of the equatorial PCNA plane, can place spatial constraints on the conformational flexibility of proteins bound to ub-PCNA. We show that ub-PCNA is impaired in its ability to support the coordinated actions of Fen1 and Pol δ in assays mimicking Okazaki fragment processing. This provides evidence for the novel concept that ub-PCNA may modulate additional DNA transactions other than TLS polymerase recruitment and switching.     

Mimicking the germinal center reaction in hybridoma cells to isolate temperature-selective anti-PEG antibodies

Modification of antibody class and binding properties typically requires cloning of antibody genes, antibody library construction, phage or yeast display and recombinant antibody expression. Here, we describe an alternative “cloning-free” approach to generate antibodies with altered antigen-binding and heavy chain isotype by mimicking the germinal center reaction in antibody-secreting hybridoma cells. This was accomplished by lentiviral transduction and controllable expression of activation-induced cytidine deaminase (AID) to generate somatic hypermutation and class switch recombination in antibody genes coupled with high-throughput fluorescence-activated cell sorting (FACS) of hybridoma cells to detect altered antibody binding properties. Starting from a single established hybridoma clone, we isolated mutated antibodies that bind to a low-temperature structure of polyethylene glycol (PEG), a polymer widely used in nanotechnology, biotechnology and pharmaceuticals. FACS of AID-infected hybridoma cells also facilitated rapid identification of class switched variants of monoclonal IgM to monoclonal IgG. Mimicking the germinal center reaction in hybridoma cells may offer a general method to identify and isolate antibodies with altered binding properties and class-switched heavy chains without the need to carry out DNA library construction, antibody engineering and recombinant protein expression.     

De novo discovery of antibody drugs – great promise demands scrutiny

ABSTRACT

We live in an era of rapidly advancing computing capacity and algorithmic sophistication. “Big data” and “artificial intelligence”find progressively wider use in all spheres of human activity, including healthcare. A diverse array of computational technologies is being applied with increasing frequency to antibody drug research and development (R&D). Their successful applications are met with great interest due to the potential for accelerating and streamlining the antibody R&D process. While this excitement is very likely justified in the long term, it is less likely that the transition from the first use to routine practice will escape challenges that other new technologies had experienced before they began to blossom. This transition typically requires many cycles of iterative learning that rely on the deconstruction of the technology to understand its pitfalls and define vectors for optimization. The study by Vasquez et al. identifies a key obstacle to such learning: the lack of transparency regarding methodology in computational antibody design reports, which has the potential to mislead the community efforts     

Reproductive biology of Bagrus docmak in the Victoria Nile,Uganda

Aspects of the reproductive biology of Bagrus docmak in the Victoria Nile were investigated between November 2005 and October 2006. Macroscopic and histological analysis of the gonads confirmed it as an asynchronous batch spawner which spawns throughout the year with bimodal spawning peaks coinciding with rainfall seasons. The first spawning peak occurred from March to May, the second from September to November. The sex ratio did not significantly deviate from 1:1. Length at sexual maturity was 33.6 cm and 31.6 cm fork length (FL) for females and males, respectively. Batch fecundity ranged from 1 000 eggs in 34 cm FL fish to 43 000 eggs in 79 cm FL fish, and correlated linearly with FL (r = 0.72) and body weight (r = 0.79). Mean relative batch fecundity was 6 eggs g^?1 (SE 2). These results could guide research into the possibility of artificially inducing the fish to spawn, and its subsequent culture.     

A tethering coherent protein in autophagosome maturation

Autophagy is a cellular pathway that degrades damaged organelles, cytosol and microorganisms, thereby maintaining human health by preventing various diseases including cancers, neurodegenerative disorders and diabetes. In autophagy, autophagosomes carrying cellular cargoes fuse with lysosomes for degradation. The proper autophagosome-lysosome fusion is pivotal for efficient autophagy activity. However, the molecular mechanism that specifically directs the fusion process is not clear. Our study reported that lysosome-localized TECPR1 (TECtonin β-Propeller Repeat containing 1) binds the autophagosome-localized ATG12–ATG5 conjugate and recruits it to autolysosomes. TECPR1 also binds PtdIns3P in an ATG12–ATG5-dependent manner. Consequently, depletion of TECPR1 leads to a severe defect in autophagosome maturation. We propose that the interaction between TECPR1 and ATG12–ATG5 initiates the fusion between the autophagosome and lysosome, and TECPR1 is a TEthering Coherent PRotein in autophagosome maturation.     

Epigenetic disorders and altered gene expression after use of Assisted Reproductive Technologies in domestic cattle

The use of Assisted Reproductive Technologies (ARTs) in modern cattle breeding is an important tool for improving the production of dairy and beef cattle. A frequently employed ART in the cattle industry is in vitro production of embryos. However, bovine in vitro produced embryos differ greatly from their in vivo produced counterparts in many facets, including developmental competence. The lower developmental capacity of these embryos could be due to the stress to which the gametes and/or embryos are exposed during in vitro embryo production, specifically ovarian hormonal stimulation, follicular aspiration, oocyte in vitro maturation in hormone supplemented medium, sperm handling, gamete cryopreservation, and culture of embryos. The negative effects of some ARTs on embryo development could, at least partially, be explained by disruption of the physiological epigenetic profile of the gametes and/or embryos. Here, we review the current literature with regard to the putative link between ARTs used in bovine reproduction and epigenetic disorders and changes in the expression profile of embryonic genes. Information on the relationship between reproductive biotechnologies and epigenetic disorders and aberrant gene expression in bovine embryos is limited and novel approaches are needed to explore ways in which ARTs can be improved to avoid epigenetic disorders.     

Melatonin protects against defects induced by malathion during porcine oocyte maturation

Malathion (MAL) is a common organophosphorus pesticide and affects both animal and human reproduction. However, the mechanisms regarding how MAL affects the mammalian oocyte quality and how to prevent it have not been fully investigated. In this study, we used porcine oocyte as a model and proved that MAL impaired porcine oocyte quality in a dose-dependent manner during maturation. MAL decreased the first polar body extrusion, disrupted spindle assembly and chromosome alignment, impaired cortical granules (CGs) distribution, and increased reactive oxygen species (ROS) level in oocytes. RNA-seq analysis showed that MAL exposure altered the expression of 2,917 genes in the porcine maturated oocytes and most genes were related to ROS, the lipid droplet process, and the energy supplement. Nevertheless, these defects could be remarkably ameliorated by adding melatonin (MLT) into the oocyte maturation medium. MLT increased oocyte maturation rate and decreased the abnormities of spindle assembly, CGs distribution and ROS accumulation in MAL-exposed porcine oocytes. More important, MLT upregulated the expression of genes related to lipid droplet metabolism (PPARγ and PLIN2), decreased lipid droplet size and lipid peroxidation in MAL-exposed porcine oocytes. Finally, we found that MLT increased the blastocysts formation and the cell numbers of blastocysts in MAL-exposed porcine oocytes after parthenogenetic activation, which was mediated by reduction of ROS levels and maintaining lipid droplet metabolism. Taken together, our results revealed that MLT had a protective action against MAL-induced deterioration of porcine oocyte quality.     

The population ecology of Rattus exulans on Tiritiri Matangi Island,and a model of comparative population dynamics in New Zealand

Abstract

On Tiritiri, a small predator-free island in northern New Zealand, kiore (Rattus exulans) were live and snap trapped in grassland and forest. In both habitats, kiore abundance peaked in late summer/autumn. The increase followed a 3 month breeding season during which females produced two to three litters, each averaging 7 young. During the population decline in autumn and winter, animals lost weight. Few bred in the breeding season of their birth and none lived to breed in a second breeding season, so the population consisted of distinct age cohorts. These patterns may relate to a highly seasonal food supply.

Kiore elsewhere in New Zealand show seasonal breeding, but the length of breeding, sexual maturation, and litter size vary. Other studies of kiore in the Pacific show less marked seasonal fluctuations, longer breeding seasons, and smaller litters. We propose a model to explain the variation in rodent demography in New Zealand. The model is based on the seasonal availability of food, along with the modifying influences of predation and dispersal.     

1-Methyladenine inhibits adenylate cyclase in starfish oocytes

Summary

The effect of 1-methyladenine (1-MeA) on adenylate cyclase (AC) basal activity and on preliminary stimulated AC activity was investigated in oocyte membrane preparations of the starfish Aphelasterias japonica. 1-MeA inhibited the membrane-bound AC activity both after its addition to intact oocytes and in cell-free experiments. GTP did not affect AC activity but it intensified the inhibitory effect of 1-MeA on AC activity. Sodium fluoride (F″) stimulated the oocyte AC (8 fold), while 1-MeA significantly reduced F″-stimulated activity. Manganese (MnCl₂, 5mM) stimulated AC (150 fold), but 1-MeA did not reduce Mn²⁺-stimulated activity. However, Mn²⁺-stimulated AC activity was inhibited by 1-MeA in the presence of MgCl₂. Forskolin stimulated AC activity (7 fold) and 1-MeA had no effect on AC. Thus, the inhibitory effect of 1-MeA on stimulated AC activity is displayed only after stimulation of the regulatory AC subunit. We suggest that 1-MeA inhibits the oocyte AC acting via inhibitory regulatory Gi protein of AC.     

Gonadal maturation,fecundity, spawning,and timing of reproduction in the mud snail,Cerithidea cingulata,a pest in milkfish ponds in the Philippines

Summary

Gonadal maturation, spawning, fecundity and timing of reproduction of the snail Cerithidea cingulata in a brackish water pond in Molo, Iloilo, Philippines, are described. Snails 4–41 mm in shell length were sampled monthly from May 1997 to May 1998; 25% were <25 mm, 67% were 20–30 mm, and 8% were >30 mm. The sexes are separate and could first be distinguished at 15 mm. Males are aphallic, have narrower shells than females of the same length, and have bright yellow-orange testes overlying the digestive gland deep inside the shell. Females have more robust shells, an ovipositor at the right side of the foot, and yellow-green ovaries overlying the digestive gland. The sex ratio was one male to two females in the pond population studied. Gonadal maturation was monitored by means of gonadosomatic index (GSI, gonad weight as a percent of visceral weight); maturation stages were based on the gonad appearance (immature, developing, mature) and histology (immature, developing, mature, redeveloping). GSI increased with snail size, and reached 16% in a 33-mm female. The smallest mature males and females were 18–19 mm, and most snails >20 mm were mature, spawning, or redeveloping. Histological sections showed all stages of gametogenesis in mature male snails. The oocyte size-frequency distributions in mature females showed mostly mature oocytes and secondary oocytes, but also oogonia and primary oocytes. GSI and the frequency of snails at different maturation stages varied over the year. Both GSI and the frequency of mature snails were highest during the summer months, April to August. Nevertheless, mature snails occurred throughout the whole year, as did mating and egg-laying. Fecundity (= number of oocytes >70 pμ) increased with size in mature females 2041 mm; an average 25-mm female produced about 1,500 oocytes and larger females produced a maximum of about 2,500 oocytes. Eggs strings laid on the pond bottom were 45–75 mm long; an average 64-mm string contained 2,000 eggs 210+20 pm in diameter. The density of eggs strings was highest (80–120/m²) during March-September. Eggs hatched after 6–7 d into planktonic veligers, which in turn settle on the pond bottom 11–12 d later as juveniles. Juveniles 2–6-mm long were most abundant in the pond during August-October.