scholarly journals Developmental expression of the 412 retrotransposon in natural populations of D. melanogaster and D. simulans

2000 ◽  
Vol 76 (3) ◽  
pp. 217-226 ◽  
Author(s):  
N. BORIE ◽  
C. LOEVENBRUCK ◽  
C. BIEMONT
Keyword(s):  
Expression Pattern ◽  
Copy Number ◽  
Developmental Stages ◽  
Population Sample ◽  
Natural Populations ◽  
Developmental Expression ◽  
Regulatory Sequences ◽  
Copy Numbers ◽  
Species Specific ◽  
Very High

We analysed the pattern of expression of retrotransposon 412 through developmental stages in various populations of Drosophila simulans and D. melanogaster differing in 412 copy number. We found that the 412 expression pattern varied greatly between populations of both species, indicating that such patterns were not entirely species-specific. In D. simulans, total transcripts increased with number of 412 copies in the chromosomes when this number was low, and then decreased for high copy numbers. D. melanogaster, which has a higher 412 copy number than D. simulans, had overall a lower global 412 expression, but again showed variation in 412 expression pattern between populations. These results suggest that in populations of D. simulans with low 412 copy number, the expression pattern of this element depends not only on copy number but also on host cellular regulatory sequences near which the elements were inserted. In D. simulans populations with high copy number overall transcription was on the contrary globally repressed, as observed in D. melanogaster. A population from Canberra (Australia) which had a very high 412 copy number was found to be associated with very high expression of 412 over all developmental stages, suggesting that the above 412 expression regulation processes are overcome in this population sample. The analysis of hybrids between geographically distinct populations of D. simulans showed that 412 expression was trans-regulated differently according to developmental stages, implying complex interactions between the 412 element and stage-specific host genes.

335 GENETIC ENGINEERING OF GOATS FOR THE PRODUCTION OF A BIOSIMILAR ANTIBODY IN MILK

2013 ◽  
Vol 25 (1) ◽  
pp. 315
Author(s):  
G. Laible ◽  
S.-A. E. Cole ◽  
B. K. Brophy ◽  
M. J. Wright ◽  
M. C. Berg ◽  
...  
Keyword(s):  
Copy Number ◽  
Simultaneous Detection ◽  
Number Line ◽  
Easy Access ◽  
Regulatory Sequences ◽  
Position Effects ◽  
Copy Numbers ◽  
Cell Clones ◽  
Fetal Fibroblasts ◽  
Transgenic Goats

Dairy animals provide an attractive production platform for biosimilar antibodies due to the high protein production capacity of the mammary gland and easy access to milk. Goats are well suited for this approach as they offer a relatively short gestation time and good milk yield and are fully validated for the production of recombinant therapeutics. To generate transgenic goats capable of producing a biosimilar version of cetuximab, a monoclonal antibody for epidermal growth factor receptor and approved for the treatment of specific cancers, we co-transfected primary female fetal fibroblasts with expression constructs for cetuximab’s heavy (HC) and light (LC) chains under the control of the goat β-casein regulatory sequences. Beta-globin insulators were added to both transgenes to minimize position effects, and an antibiotic selection marker was placed downstream of the HC transgene sequences to allow for the isolation of stable transgenic cell clones. Selected cell clones were screened by PCR for the presence of both transgenes. Positive cell clones were analysed by Southern blot with a β-casein-specific probe. This allowed for the simultaneous detection of both transgenes, and the endogenous β-casein gene served as a standard to determine transgene copy numbers. The cell clones showed a broad range of copy numbers, from single copy insertions to >100 copies for the HC and LC transgenes. Interestingly, most of the cell clones had more LC than HC transgene copies. Ten cell clones were selected to generate transgenic founders using somatic cell nuclear transfer. We were able to produce 43 live kids from 9 cell lines following transfer of between 26 and 153 one- and two-cell embryos per line into recipients (range of 4 to 15 embryos per recipient). The one cell clone that we used unsuccessfully had the lowest number of transferred embryos (11). The efficiency for the production of live kids per transferred embryos was, on average, 5.1% (range of 1.0 to 9.7%). Kids from 5 lines were hormonally induced into lactation at the age of 10 weeks. Two lines with high copy numbers (≥30) produced either no or only a few drops of milk, whereas the lines with ≤25 transgene copies gave up to several milliliters of milk per day. Western analyses confirmed cetuximab production levels of 15 g L–1 in 2 of the lines with ≤25 transgene copies and ~45 g L–1 in a high copy number line; one low copy number line showed good HC but very low LC expression. Our data demonstrate that cetuximab can be produced in significant quantities in transgenic goats. Future work is aimed at determining production levels under natural lactation conditions and characterising glycosylation patterns to fully understand the pharmacodynamic properties of the antibody. Supported by GTC, the NZ Ministry of Science and Innovation and AgResearch.

scholarly journals Sexual and developmental variations of ecto-parasitism in damselflies

2021 ◽  
Author(s):  
Shatabdi Paul ◽  
Md Kawsar Khan ◽  
Marie E. Herberstein
Keyword(s):  
Body Condition ◽  
Developmental Stages ◽  
Natural Populations ◽  
Parasite Load ◽  
Parasite Prevalence ◽  
Total Body Length ◽  
Developmental Differences ◽  
Males And Females ◽  
Developmental Variations ◽  
Species Specific

AbstractThe prevalence and intensity of parasitism can have different fitness costs between sexes, and across species and developmental stages. This variation could arise because of species specific sexual and developmental differences in body condition, immunity, and resistance. Theory predicts that the prevalence of parasitism will be greater in individuals with poor body condition and the intensity of parasitism will be greater in individuals with larger body size. These predictions have been tested and verified in vertebrates. In insects, however, contradictory evidence has been found in different taxa. Here, we tested these predictions on two species of Agriocnemis (Agriocnemis femina and Agriocnemis pygmaea) damselflies, which are parasitized by Arrenurus water mite ectoparasites. We measured body weight, total body length, abdomen area and thorax area of non-parasitized damselflies and found body condition varied between males and females, between immature females and mature females and between A. femina and A. pygmaea. Then, we calculated the parasite prevalence, i.e., the frequency of parasitism and intensity, i.e., the number of parasites per infected damselfly in eleven natural populations of both species. In line to our predictions, we observed greater prevalence in immature females than mature females but found no difference in parasite prevalence between males and females. Furthermore, we found that parasite load was higher in females than males and in immature females than mature females. Our result also showed that the frequency and intensity of parasitism varied between the two studied species, being higher in A. pygmaea than A. femina. Our study provides evidence that parasitism impacts sexes, developmental stages and species differentially and suggests that variation may occur due to sex, developmental stage, and species-specific resistance and tolerance mechanism.

scholarly journals The relationship between the rate of transposition and transposable element copy number for copia and Doc retrotransposons of Drosophila melanogaster

1998 ◽  
Vol 72 (1) ◽  
pp. 1-11 ◽  
Author(s):  
ELENA G. PASYUKOVA ◽  
SERGEY V. NUZHDIN ◽  
DMITRY A. FILATOV
Keyword(s):  
Drosophila Melanogaster ◽  
Copy Number ◽  
Self Regulation ◽  
Natural Populations ◽  
Strong Positive Correlation ◽  
Positive Correlation ◽  
Transposition Rate ◽  
Copy Numbers ◽  
Starting Point ◽  
The Relationship

We present data on the relationship between the rate of transposition and copy number in the genome for the copia and Doc retrotransposons of Drosophila melanogaster. copia and Doc transposition rates were directly measured in sublines of the isogenic 2b line using individual males or females, respectively, with a range of copia copy numbers from 49 to 103 and Doc copy numbers from 112 to 235 per genome. Transposition rates varied from 3×10−4 to 2×10−2 for copia and from 2×10−4 to 2×10−3 for Doc. A positive relationship between transposition rate and copy number was found both for copia and for Doc when the data were analysed across all the 2b individuals; no significant correlation was found when the data were analysed across the subline means for both retrotransposons tested. Overall, correlation between copia and Doc transposition rate and their copy number in the genome, if any, was not negative, which would be expected if transposable elements (TEs) self-regulate their copy number. Thus, for copia and Doc no evidence for self-regulation was provided, and at least for these two TEs this hypothesis is not favoured for explaining the maintenance of the stable copy number that is characteristic for natural populations. The transposition rate of copia was measured twice, and a strong positive correlation between copy number and transposition rate both across individuals and subline means was found in 1994, while in 1995 no correlation was found. This fact is in agreement with the hypothesis that a positive correlation between the rate of transposition and TE copy number may be a default starting point for future host–TE coevolution.

scholarly journals A multi-bioassay integrated approach to assess antifouling potential of extracts from the Mediterranean sponge Ircinia oros

2021 ◽  
Author(s):  
Lucia De Marchi ◽  
Carlo Pretti ◽  
Alessia Cuccaro ◽  
Matteo Oliva ◽  
Federica Tardelli ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Integrated Approach ◽  
Common Species ◽  
Marine Diatom ◽  
Cellular Damage ◽  
Inhibition Of Growth ◽  
Aliivibrio Fischeri ◽  
The Mediterranean ◽  
Ircinia Oros ◽  
Species Specific

AbstractThe phylum Porifera and their symbionts produce a wide variety of bioactive compounds, playing a central role in their ecology and evolution. In this study, four different extracts (obtained by non-polar and semi-polar extraction methodologies) of the Mediterranean sponge Ircinia oros were tested through a multi-bioassay integrated approach to assess their antifouling potential. Tests were performed using three common species, associated with three different endpoints: the marine bacterium Aliivibrio fischeri (inhibition of bioluminescence), the marine diatom Phaeodactylum tricornutum (inhibition of growth), and different development stages of the brackish water serpulid Ficopomatus enigmaticus (gametes: sperm motion, vitality inhibition and cellular damage; larvae: development; adults: AChE (acetylcholinesterase)-inhibitory activity). The effects of extracts were species specific and did not vary among different extraction methodologies. In particular, no significant reduction of bioluminescence of A. fischeri was observed for all tested samples. By contrast, extracts inhibited P. tricornutum growth and had toxic effects on different F. enigmaticus’ developmental stages. Our results suggest that the proposed test battery can be considered a suitable tool as bioactivity screening of marine natural products.

scholarly journals The Effect of an Anthropogenic Magnetic Field on the Early Developmental Stages of Fishes—A Review

2021 ◽  
Vol 22 (3) ◽  
pp. 1210
Author(s):  
Krzysztof Formicki ◽  
Agata Korzelecka-Orkisz ◽  
Adam Tański
Keyword(s):  
Magnetic Fields ◽  
Developmental Stages ◽  
Negative Influence ◽  
Pigment Cells ◽  
Egg Activation ◽  
Industrial Equipment ◽  
Positive Effects ◽  
Early Developmental Stages ◽  
Species Specific ◽  
Early Developmental

The number of sources of anthropogenic magnetic and electromagnetic fields generated by various underwater facilities, industrial equipment, and transferring devices in aquatic environment is increasing. These have an effect on an array of fish life processes, but especially the early developmental stages. The magnitude of these effects depends on field strength and time of exposure and is species-specific. We review studies on the effect of magnetic fields on the course of embryogenesis, with special reference to survival, the size of the embryos, embryonic motor function, changes in pigment cells, respiration hatching, and directional reactions. We also describe the effect of magnetic fields on sperm motility and egg activation. Magnetic fields can exert positive effects, as in the case of the considerable extension of sperm capability of activation, or have a negative influence in the form of a disturbance in heart rate or developmental instability in inner ear organs.

scholarly journals Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xinping Fan ◽  
Guanghao Luo ◽  
Yu S. Huang
Keyword(s):  
Copy Number ◽  
Bayesian Learning ◽  
Kernel Smoothing ◽  
Gaussian Mixture ◽  
Copy Number Alterations ◽  
Sequencing Data ◽  
Copy Numbers ◽  
Allele Specific ◽  
Tumor Sequencing ◽  
Low Coverage

Abstract Background Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. Results We introduce Accucopy, a method to infer total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy adopts many robust statistical techniques such as kernel smoothing of coverage differentiation information to discern signals from noise and combines ideas from time-series analysis and the signal-processing field to derive a range of estimates for the period in a histogram of coverage differentiation information. Statistical learning models such as the tiered Gaussian mixture model, the expectation–maximization algorithm, and sparse Bayesian learning were customized and built into the model. Accucopy is implemented in C++ /Rust, packaged in a docker image, and supports non-human samples, more at http://www.yfish.org/software/. Conclusions We describe Accucopy, a method that can predict both TCNs and ASCNs from low-coverage low-purity tumor sequencing data. Through comparative analyses in both simulated and real-sequencing samples, we demonstrate that Accucopy is more accurate than Sclust, ABSOLUTE, and Sequenza.

scholarly journals HiCancer: accurate and complete cancer genome phasing with Hi-C reads

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weihua Pan ◽  
Desheng Gong ◽  
Da Sun ◽  
Haohui Luo
Keyword(s):  
Copy Number ◽  
Somatic Mutations ◽  
Copy Number Variations ◽  
Cancer Genome ◽  
Structural Variations ◽  
Genome Map ◽  
Linkage Information ◽  
Suboptimal Solution ◽  
Allelic Copy Number ◽  
Very High

AbstractDue to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HiCancer. HiCancer solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.

scholarly journals Development and Interrogation of a Transcriptomic Resource for the Giant Triton Snail (Charonia tritonis)

2021 ◽  
Author(s):  
AH Klein ◽  
CA Motti ◽  
AK Hillberg ◽  
T Ventura ◽  
P Thomas-Hall ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Cell Signalling ◽  
Natural Populations ◽  
Olfactory Receptors ◽  
Gill Tissue ◽  
Abundant Species ◽  
Population Outbreaks ◽  
Coral Reef Ecosystems ◽  
Specialist Predators ◽  
G Protein Coupled

AbstractGastropod molluscs are among the most abundant species that inhabit coral reef ecosystems. Many are specialist predators, along with the giant triton snail Charonia tritonis (Linnaeus, 1758) whose diet consists of Acanthaster planci (crown-of-thorns starfish), a corallivore known to consume enormous quantities of reef-building coral. C. tritonis are considered vulnerable due to overexploitation, and a decline in their populations is believed to have contributed to recurring A. planci population outbreaks. Aquaculture is considered one approach that could help restore natural populations of C. tritonis and mitigate coral loss; however, numerous questions remain unanswered regarding their life cycle, including the molecular factors that regulate their reproduction and development. In this study, we have established a reference C. tritonis transcriptome derived from developmental stages (embryo and veliger) and adult tissues. This was used to identify genes associated with cell signalling, such as neuropeptides and G protein-coupled receptors (GPCRs), involved in endocrine and olfactory signalling. A comparison of developmental stages showed that several neuropeptide precursors are exclusively expressed in post-hatch veligers and functional analysis found that FFamide stimulated a significant (20.3%) increase in larval heart rate. GPCRs unique to veligers, and a diversity of rhodopsin-like GPCRs located within adult cephalic tentacles, all represent candidate olfactory receptors. In addition, the cytochrome P450 superfamily, which participates in the biosynthesis and degradation of steroid hormones and lipids, was also found to be expanded with at least 91 genes annotated, mostly in gill tissue. These findings further progress our understanding of C. tritonis with possible application in developing aquaculture methods.

scholarly journals Going Wild: Lessons from Naturally Occurring T-Lymphotropic Lentiviruses

2006 ◽  
Vol 19 (4) ◽  
pp. 728-762 ◽  
Author(s):  
Sue VandeWoude ◽  
Cristian Apetrei
Keyword(s):  
Immune Responses ◽  
Natural Populations ◽  
Host Immune Responses ◽  
Experimental Systems ◽  
Naturally Occurring ◽  
Immunodeficiency Virus ◽  
New Directions ◽  
Species Specific ◽  
Lentiviral Infections ◽  
Hiv Aids

SUMMARY Over 40 nonhuman primate (NHP) species harbor species-specific simian immunodeficiency viruses (SIVs). Similarly, more than 20 species of nondomestic felids and African hyenids demonstrate seroreactivity against feline immunodeficiency virus (FIV) antigens. While it has been challenging to study the biological implications of nonfatal infections in natural populations, epidemiologic and clinical studies performed thus far have only rarely detected increased morbidity or impaired fecundity/survival of naturally infected SIV- or FIV-seropositive versus -seronegative animals. Cross-species transmissions of these agents are rare in nature but have been used to develop experimental systems to evaluate mechanisms of pathogenicity and to develop animal models of HIV/AIDS. Given that felids and primates are substantially evolutionarily removed yet demonstrate the same pattern of apparently nonpathogenic lentiviral infections, comparison of the biological behaviors of these viruses can yield important implications for host-lentiviral adaptation which are relevant to human HIV/AIDS infection. This review therefore evaluates similarities in epidemiology, lentiviral genotyping, pathogenicity, host immune responses, and cross-species transmission of FIVs and factors associated with the establishment of lentiviral infections in new species. This comparison of consistent patterns in lentivirus biology will expose new directions for scientific inquiry for understanding the basis for virulence versus avirulence.

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