A novel insertional allele of the CG18135 gene is associated with severe mutant phenotypes in Drosophila melanogaster.

Drosophila melanogaster has been at the forefront of genetic studies and biochemical modeling for over a century. Yet, the functions of many genes are still unknown, mainly because no phenotypic data are available. Herein, we present the first evidence data regarding the particular molecular and other quantifiable phenotypes, such as viability and anatomical anomalies, induced by a novel P{lacW} insertional mutant allele of the CG18135 gene. So far, the CG18135 functions have only been theorized based on electronic annotation and presumptive associations inferred upon high-throughput proteomics or RNA sequencing experiments. The descendants of individuals harboring the CG18135 P{lacW}CG18135 allele were scored in order to assess mutant embryonic, larval, and pupal viability versus Canton Special (CantonS). Our results revealed that the homozygous CG18135 P{lacW}CG18135 /CG18135 P{lacW}CG18135 genotype determines significant lethality both at the inception of the larval stage and during pupal development. The very few imago escapers that either breach or fully exit the puparium exhibit specific eye depigmentation, wing abnormal unfolding, strong locomotor impairment with apparent spasmodic leg movements, and their maximum lifespan is shorter than 2 days. Using the quantitative real-time PCR (qRT-PCR) method, we found that CG18135 is upregulated in male flies, but an unexpected gene upregulation was also detected in heterozygous mutants compared to wild-type flies, probably because of regulatory perturbations induced by the P{lacW} transposon. Our work provides the first phenotypic evidence for the essential role of CG18135, a scenario in accordance with the putative role of this gene in carbohydrate-binding processes.

Longitudinal in Utero Analysis of Engrailed-1 Knockout Mouse Embryonic Phenotypes Using High-Frequency Ultrasound.

Large-scale international efforts to generate and analyze loss-of-function mutations in each of the approximately 20,000 protein-encoding gene mutations are ongoing using the "knockout" mouse as a model organism. Because one-third of gene knockouts are expected to result in embryonic lethality, it is important to develop non-invasive in utero imaging methods to detect and monitor mutant phenotypes in mouse embryos. We describe the utility of 3-D high-frequency (40-MHz) ultrasound (HFU) for longitudinal in utero imaging of mouse embryos between embryonic days (E) 11.5 and E14.5, which represent critical stages of brain and organ development. Engrailed-1 knockout (En1-ko) mouse embryos and their normal control littermates were imaged with HFU in 3-D, enabling visualization of morphological phenotypes in the developing brains, limbs and heads of the En1-ko embryos. Recently developed deep learning approaches were used to automatically segment the embryonic brain ventricles and bodies from the 3-D HFU images, allowing quantitative volumetric analyses of the En1-ko brain phenotypes. Taken together, these results show great promise for the application of longitudinal 3-D HFU to analyze knockout mouse embryos in utero.

Rapid Intraspecies Evolution of Fitness Effects of Yeast Genes.

Organisms within species have numerous genetic and phenotypic variations. Growing evidences show intraspecies variation of mutant phenotypes may be more complicated than expected. Current studies on intraspecies variations of mutant phenotypes are limited to just a few strains. This study investigated the intraspecies variation of fitness effects of 5,630 gene mutants in ten Saccharomyces cerevisiae strains using CRISPR-Cas9 screening. We found that the variability of fitness effects induced by gene disruptions is very large across different strains. Over 75% of genes affected cell fitness in a strain-specific manner to varying degrees. The strain specificity of the fitness effect of a gene is related to its evolutionary and functional properties. Subsequent analysis revealed that younger genes, especially those newly acquired in S. cerevisiae species, are more likely to be strongly strain-specific. Intriguingly, there seems to exist a ceiling of fitness effect size for strong strain-specific genes, and among them, the newly acquired genes are still evolving and have yet to reach this ceiling. Additionally, for a large proportion of protein complexes, the strain specificity profile is inconsistent among genes encoding the same complex. Taken together, these results offer a genome-wide map of intraspecies variation for fitness effect as a mutant phenotype and provide an updated insight on intraspecies phenotypic evolution.

Mutant Phenotype p53 Immunohistochemical Expression Is Associated With Poor Prognostic Parameters and Disease-Free Survival in Triple-Negative Metaplastic Breast Carcinoma.

Introduction Metaplastic breast carcinoma (MBC) is a special type of breast cancer that is most commonly triple-negative and has the worst outcome compared to other breast tumors. p53 is a tumor suppressor gene that is frequently mutated in many human cancers. The association of mutant p53 immunohistochemical expression with clinical and prognostic parameters has not been widely studied in triple-negative MBC. Therefore, in this study, we evaluated the expression patterns of p53 in triple-negative MBC and its association with clinical and prognostic parameters. Methods A retrospective observational study was conducted in the Department of Histopathology at Liaquat National Hospital and Medical College, Pakistan, for a duration of 11 years. A total of 101 cases of triple-negative MBCs were included in the study. p53 immunohistochemistry was performed on the representative tissue blocks. Cases with diffuse strong positive p53 expression were labeled mutant phenotype, while cases with weak patchy p53 expression were termed wild-type. Results The mean age of the patients was 48.33±11.47 years, and the mean tumor size was 3.98±2.07 cm. The mean Ki67 index was 48.98±22.97%. The median disease-free survival of the patients was 24 (three to 68) months, with a median follow-up of 37 (13 to 77) months. Most of the cases were tumor (T)-stage II (51.5%). Axillary metastasis was present in 36.6% of cases, with the perinodal extension in 16.8% of cases. Most cases were non-basal subtype (91.1%), and the majority of cases were grade III (85.1%). Recurrence was observed in 17.8% of cases. Among 101 cases, 52.5% cases showed mutant phenotype p53 expression. A significant association of p53 expression was noted with tumor grade, Ki67 index and disease-free survival. Cases with mutant phenotype p53 expression had a higher tumor grade, higher Ki67 index, and poorer disease-free survival than cases with wild-type p53 expression. Conclusion A substantial proportion of triple-negative MBC expressed diffuse strong expression (mutant phenotype) of p53 in our study, signifying a potential role of p53 as a therapeutic target in triple-negative MBC. Moreover, association of p53 with poor prognostic parameters, such as higher tumor grade and Ki67, and poor disease-free survival underscores the prognostic significance of p53 in triple-negative MBC.

Practicing logical reasoning through Drosophila segmentation gene mutants.

Laboratory practical sessions are critical to scientific training in biology but usually fail to promote logical and hypothesis-driven reasoning and rely heavily on the teacher's instructions. This paper describes a 2-day laboratory practicum in which students prepare and analyze larval cuticle preparations of Drosophila segmentation gene mutant strains. Embryonic segmentation involves three major classes of genes according to their loss-of-function phenotypes: the establishment of broad regions by gap genes, the specification of the segments by the pair-rule genes, and the compartments within segments by the segment polarity genes. Students are asked to sort undefined segmentation mutants into gap, pair-rule, or segment polarity categories based on their knowledge of the Drosophila segmentation process and the microscopic anatomical traits they are capable of finding in the sample preparations. This technically simple practicum prompts students to pay attention to detailed observation to detect anatomic markers of intrasegmental compartments and thorax versus abdomen cuticle, and promote their logical reasoning in hypothesizing to which segmentation type a given mutant fits best.

Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon Sulfolobus islandicus.

Proteins undergo acetylation at the Nε-amino group of lysine residues and the Nα-amino group of the N terminus in Archaea as in Bacteria and Eukarya. However, the extent, pattern and roles of the modifications in Archaea remain poorly understood. Here we report the proteomic analyses of a wild-type Sulfolobus islandicus strain and its mutant derivative strains lacking either a homolog of the protein acetyltransferase Pat (ΔSisPat) or a homolog of the Nt-acetyltransferase Ard1 (ΔSisArd1). A total of 1708 Nε-acetylated lysine residues in 684 proteins (26% of the total proteins), and 158 Nt-acetylated proteins (44% of the identified proteins) were found in S. islandicus ΔSisArd1 grew more slowly than the parental strain, whereas ΔSisPat showed no significant growth defects. Only 24 out of the 1503 quantifiable Nε-acetylated lysine residues were differentially acetylated, and all but one of the 24 residues were less acetylated by >1.3 fold in ΔSisPat than in the parental strain, indicating the narrow substrate specificity of the enzyme. Six acyl-CoA synthetases were the preferred substrates of SisPat in vivo, suggesting that Nε-acetylation by the acetyltransferase is involved in maintaining metabolic balance in the cell. Acetylation of acyl-CoA synthetases by SisPat occurred at a sequence motif conserved among all three domains of life. On the other hand, 92% of the acetylated N termini identified were acetylated by SisArd1 in the cell. The enzyme exhibited broad substrate specificity and could modify nearly all types of the target N termini of human NatA-NatF. The deletion of the SisArd1 gene altered the cellular levels of 18% of the quantifiable proteins (1518) by >1.5 fold. Consistent with the growth phenotype of ΔSisArd1, the cellular levels of proteins involved in cell division and cell cycle control, DNA replication, and purine synthesis were significantly lowered in the mutant than those in the parental strain.

Cell lineage of timed cohorts of Tbx6-expressing cells in wild-type and Tbx6 mutant embryos.

Tbx6 is a T-box transcription factor with multiple roles in embryonic development as evidenced by dramatic effects on mesoderm cell fate determination, left/right axis determination, and somite segmentation in mutant mice. The expression of Tbx6 is restricted to the primitive streak and presomitic mesoderm, but some of the phenotypic features of mutants are not easily explained by this expression pattern. We have used genetically-inducible fate mapping to trace the fate of Tbx6-expressing cells in wild-type and mutant embryos to explain some of the puzzling features of the mutant phenotype. We created an inducible Tbx6-creERT2 transgenic mouse in which cre expression closely recapitulates endogenous Tbx6 expression both temporally and spatially. Using a lacZ-based Cre reporter and timed tamoxifen injections, we followed temporally overlapping cohorts of cells that had expressed Tbx6 and found contributions to virtually all mesodermally-derived embryonic structures as well as the extraembryonic allantois. Contribution to the endothelium of major blood vessels may account for the embryonic death of homozygous mutant embryos. In mutant embryos, Tbx6-creERT2-traced cells contributed to the abnormally segmented anterior somites and formed the characteristic ectopic neural tubes. Retention of cells in the mutant tail bud indicates a deficiency in migratory behavior of the mutant cells and the presence of Tbx6-creERT2-traced cells in the notochord, a node derivative provides a possible explanation for the heterotaxia seen in mutant embryos.

Specialized Information Processing Deficits and Distinct Metabolomic Profiles Following TM-Domain Disruption of Nrg1.

Although there is considerable genetic and pathologic evidence for an association between neuregulin 1 (NRG1) dysregulation and schizophrenia, the underlying molecular and cellular mechanisms remain unclear. Mutant mice containing disruption of the transmembrane (TM) domain of the NRG1 gene constitute a heuristic model for dysregulation of NRG1-ErbB4 signaling in schizophrenia. The present study focused on hitherto uncharacterized information processing phenotypes in this mutant line. Using a mass spectrometry-based metabolomics approach, we also quantified levels of unique metabolites in brain. Across 2 different sites and protocols, Nrg1 mutants demonstrated deficits in prepulse inhibition, a measure of sensorimotor gating, that is, disrupted in schizophrenia; these deficits were partially reversed by acute treatment with second, but not first-, generation antipsychotic drugs. However, Nrg1 mutants did not show a specific deficit in latent inhibition, a measure of selective attention that is also disrupted in schizophrenia. In contrast, in a "what-where-when" object recognition memory task, Nrg1 mutants displayed sex-specific (males only) disruption of "what-when" performance, indicative of impaired temporal aspects of episodic memory. Differential metabolomic profiling revealed that these behavioral phenotypes were accompanied, most prominently, by alterations in lipid metabolism pathways. This study is the first to associate these novel physiological mechanisms, previously independently identified as being abnormal in schizophrenia, with disruption of NRG1 function. These data suggest novel mechanisms by which compromised neuregulin function from birth might lead to schizophrenia-relevant behavioral changes in adulthood.

Closing the translational gap between mutant mouse models and the clinical reality of psychotic illness.

As animal models of psychotic illness become more refined, mutant mouse models have become increasingly prominent through their ability to inform on the structural, cellular and behavioural roles of genes associated with risk for psychosis via the phenotypic consequences of disruption of those genes. This review will consider recent advances in the field whereby mutant mouse models seek to reflect increasing knowledge of psychotic illness, focusing on four main themes. Firstly, recent GWAS and rare variant analyses have identified that disease-associated targets have not been previously implicated, thereby representing novel biological pathways in the illness, and this has implications for the modelling field. Secondly, the psychosis is disrespectful to conventional diagnostic boundaries, both clinically and in terms of pathobiology: it extends beyond schizophrenia to include several diagnostic categories and may be best captured in terms of psychopathological dimensions rather than/additional to such categories. Thirdly, a given risk gene (G) does not operate in isolation but, rather, appears to participate in complex interactions with environmental (E) risk factors, i.e., G×E interactions. Lastly, a given risk gene is likely to participate in complex, epistatic interactions with other risk genes, i.e., G×G interactions. Such studies constitute important steps in closing the translational gap between mutant mouse models and the clinical reality of psychotic illness.

The yeast deletion collection: a decade of functional genomics.

The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MAT A: and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general.

Do individually ventilated cage systems generate a problem for genetic mouse model research?

Technological developments over recent decades have produced a novel housing system for laboratory mice, so-called 'individually ventilated cage' (IVC) systems. IVCs present a cage environment which is different to conventional filter-top cages (FILTER). Nothing is known about the consequences of IVC housing on genetic mouse models, despite studies reporting IVC-mediated changes to the phenotypes of inbred mouse strains. Thus, in this study, we systematically compared the established behavioural phenotype of a validated mouse model for the schizophrenia risk gene neuregulin 1 (TM Nrg1 HET) kept in FILTER housing with Nrg1 mutant mice raised in IVC systems. We found that particular schizophrenia-relevant endophenotypes of TM Nrg1 HETs which had been established and widely published using FILTER housing were altered when mice were raised in IVC housing. IVCs diminished the schizophrenia-relevant prepulse inhibition deficit of Nrg1 mutant males. Furthermore, IVC housing had a sex-dependent moderate effect on the locomotive phenotype of Nrg1 mice across test paradigms. Behavioural effects of IVC housing were less prominent in female mice. Thus, transferring the breeding colony of mouse mutants from FILTER to IVC systems can shift disease-relevant behaviours and therefore challenge the face validity of these mice. Researchers facing an upgrade of their mouse breeding or holding facilities to IVC systems must be aware of the potential impact this upgrade might have on their genetic mouse models. Future publications should provide more details on the cage system used to allow appropriate data comparison across research sites.

Length quantization of DNA partially expelled from heads of a bacteriophage T3 mutant.

DNA packaging of phages phi29, T3 and T7 sometimes produces incompletely packaged DNA with quantized lengths, based on gel electrophoretic band formation. We discover here a packaging ATPase-free, in vitro model for packaged DNA length quantization. We use directed evolution to isolate a five-site T3 point mutant that hyper-produces tail-free capsids with mature DNA (heads). Three tail gene mutations, but no head gene mutations, are present. A variable-length DNA segment leaks from some mutant heads, based on DNase I-protection assay and electron microscopy. The protected DNA segment has quantized lengths, based on restriction endonuclease analysis: six sharp bands of DNA missing 3.7-12.3% of the last end packaged. Native gel electrophoresis confirms quantized DNA expulsion and, after removal of external DNA, provides evidence that capsid radius is the quantization-ruler. Capsid-based DNA length quantization possibly evolved via selection for stalling that provides time for feedback control during DNA packaging and injection.

A thymidine kinase-negative bovine herpesvirus 5 is highly attenuated for rabbits, but is neuroinvasive and establishes latent infection / Cepa do herpesvírus bovino tipo 5 defectiva na timidina quinase é altamente atenuada para coelhos mas é neuroinvasiva e estabelece infecção latente

Mutant viral strains deleted in non-essential genes represent useful tools to study the function of specific gene products in the biology of the virus. We herein describe an investigation on the phenotype of a bovine herpesvirus 5 (BoHV-5) recombinant deleted in the gene encoding the enzyme thymidine kinase (TK) in rabbits, with special emphasis to neuroinvasiveness and the ability to establish and reactivate latent infection. Rabbits inoculated with the parental virus (SV-507/99) (n=18) at a low titer (10(5.5)TCID50) shed virus in nasal secretions in titers up to 10(4.5)TCID50 for up to 12 days (average: 9.8 days [5-12]) and 5/ 16 developed neurological disease and were euthanized in extremis. Rabbits inoculated with the recombinant BoHV-5TKΔ at a high dose (10(7.1)TCID50) also shed virus in nasal secretions, yet to lower titers (maximum: 10(2.3)TCID50) and for a shorter period (average: 6.6 days [2-11]) and remained healthy. PCR examination of brain sections of inoculated rabbits at day 6 post-infection (pi) revealed a widespread distribution of the parental virus, whereas DNA of the recombinant BoHV-5TKΔ-was detected only in the trigeminal ganglia [TG] and olfactory bulbs [OB]. Nevertheless, during latent infection (52pi), DNA of the recombinant virus was detected in the TGs, OBs and also in other areas of the brain, demonstrating the ability of the virus to invade the brain. Dexamethasone (Dx) administration at day 65 pi was followed by virus reactivation and shedding by 5/8 rabbits inoculated with the parental strain (mean duration of 4.2 days [1 - 9]) and by none of seven rabbits inoculated with the recombinant virus. Again, PCR examination at day 30 post-Dx treatment revealed the presence of latent DNA in the TGs, OBs and in other areas of the brain of both groups. Taken together, these results confirm that the recombinant BoHV-5TKΔ is highly attenuated for rabbits. It shows a reduced ability to replicate in the nose but retains the ability...

Cepas virais mutantes defectivas em genes não essenciais se constituem em ferramentas úteis para o estudo da função de proteínas virais na biologia dos vírus. Este estudo relata uma investigação do fenótipo, em coelhos, de uma cepa recombinante do herpesvírus bovino tipo 5 (BoHV-5) defectiva na enzima timidina quinase (TK), com ênfase para a neuroinvasividade e capacidade de estabelecer e reativar a infecção latente. Coelhos inoculados com o vírus parental (SV-507/99, n=18) em baixo título (10(5,5)TCID50) excretaram o vírus nas secreções nasais em títulos de até 10(4,5)TCID50/ mL por até 12 dias (média: 9,8 dias [5-12]) e 5/16 desenvolveram doença neurológica e morreram ou foram eutanasiados in extremis. Em contraste, coelhos inoculados com o recombinante BoHV-5TKΔ em alto título (10(7,1)TCID50) excretaram o vírus em títulos inferiores (máximo 10(2,3)TCID50/ mL), por um período menor (média: 6,6 days [2-11]) e permaneceram saudáveis. A realização de PCR em seções do encéfalo no dia 6 pós-infecção (pi) revelou uma ampla distribuição do DNA do vírus parental, enquanto o DNA do vírus recombinante foi detectado apenas nos gânglios trigêmeos [TGs] e nos bulbos olfatórios [OBs]. Não obstante, durante a infecção latente (52pi), o DNA do vírus recombinante foi detectado nos TGs, OBs e em outros locais do encéfalo, demonstrando que o vírus recombinante mantém a neuroinvasividade. Tratamento com dexamethasona (Dx) no dia 65 pi resultou em reativação e excreção viral por 5/8 dos coelhos inoculados com o vírus parental (duração média de 4,2 dias [1-9]) e por nenhum dos sete coelhos inoculados com o vírus recombinante. No entanto, PCR realizado no dia 30 pós-Dx revelou a presença de DNA latente do BoHV-5TKΔ nos TGs, OBs e em outras áreas do encéfalo. Esses resultados confirmam que o recombinante BoHV-5TKΔ é altamente atenuado para coelhos. A sua capacidade de replicação na mucosa nasal é reduzida, mas mantém a capacidade de invadir o encéfalo e estabelecer infecção...