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The postharvest pathogen Penicillium digitatum is responsible for green mold decay on citrus fruit causing important economic losses. To examine possible elements involved in fungal pathogenesis/virulence and fungicide resistance, identification and functional characterization of PdSte12, a particular type of C2H2 fungal transcription factor was carried out. PdSte12 was functionally inactivated through homologous recombination. The deletant fungal strains (ΔPdSte12) failed to cause green mold decay on citrus fruit. ΔPdSte12 mutants exhibited reduced growth and impaired conidiogenesis during fungal infection towards citrus fruit. Additionally, PdSte12 was characterized via overexpression transformants, showing higher infectivity rate in a low virulence P. digitatum strain, providing evidence of PdSte12 ’s role in virulence. Moreover, fungicide sensitivity evaluation showed that PdSte12 was not involved in fungicide resistance as other transcription factors are. These results indicate that the PdSte12 transcription factor controls invasive growth and asexual reproduction as the major virulence function. [ABSTRACT FROM AUTHOR]

Aureobasidium melanogenum HN6.2 was found to able to produce an esterase of 208.1 ± 2.7 units per ml within 72 h. A molecular weight of the purified esterase was 60.2 kDa and its PI was 4.86. The optimal pH and temperature of the purified esterase were 8.0 and 40 °C, respectively. The purified esterase was stable at the temperature less than 40 °C and in the pH range of 7.5–8.0. The esterase activity was greatly inhibited in the presence of Zn 2+ , Hg 2+ , Fe 2+ , Ni 2+ and SDS. K m and V max values of the enzyme for ρ-nitrophenyl butyrate were 68.6 μM and 251.4 μM per min, respectively. Mass analysis showed that it belonged to a carboxylesterase. After an esterase gene ( Car-Est ) cloned from the genomic DNA of the marine yeast strain HN6.2 was disrupted, the disruptant Y44 obtained exhibited a significant decrease in esterase activity. Meanwhile, a transcriptional level of the Car-Est gene of the disruptant Y44 was only 5.18% that of the Car-Est gene of its wild type strain HN6.2, confirming that the cloned esterase gene was indeed closely related to the esterase activity of the yeast HN6.2 strain. [ABSTRACT FROM AUTHOR]

BACKGROUND: Our recent genetic study as well as robust evidences reported by previous genome-wide association studies (GWASs) have indicated that the single nucleotide polymorphism rs16998073, located near gene anthrax toxin receptor 2 (ANTXR2), was significantly associated with hypertension in Asians and Europeans. The aim of the present study was to determine whether ANTXR2 is the causal gene of hypertension at the 4q21 locus using an ANTXR2 knockout model. METHODS: Relative expression of ANTXR2 in Wistar-Kyoto rats (WKYs) and spontaneously hypertensive rats (SHRs) were determined by real-time quantitative polymerase chain reaction and western blot analysis. ANTXR2 knock-out rats were created using CRISPR/Cas9-mediated genome editing and blood pressure values were measured in ANTXR2-/- and wild type (WT) rats by tail-cuff method and carotid arterial catheterization method. RESULTS: Neither the mRNA nor protein levels of ANTXR2 were significantly different between tissues from SHRs and WKYs. To create ANTXR2-/- rats, 67 base pairs were deleted in exon 1 of ANTXR2 using CRISPR/Cas9-mediated genome editing. ANTXR2 protein decreased significantly in aortas of ANTXR2-/- rats, suggesting sufficient efficiency of ANTXR2 knock-out in this model. However, ANTXR2-/- rats exhibited nearly the same blood pressure as WT rats at baseline conditions as well as during Angiotensin II (400 ng/kg/min) infusion or high-salt diet treatment. CONCLUSIONS: These findings suggest that ANTXR2 might not be associated with hypertension and thus further functional analysis is warranted to identify the causal gene at this locus. [ABSTRACT FROM AUTHOR]

In this study, the function of a non-ribosomal peptide synthetase-like (NRPS-like) encoding gene AOL_s00188g306 ( g306 ) was investigated to reveal the association between NRPS and nematocidal activity in the nematode-trapping fungus Arthrobotrys oligospora . Sequence analysis indicated that the encoded product of g306 is an adenylation domain of non-ribosomal peptide synthetases and extended short-chain dehydrogenase/reductase domain-containing proteins, and displays a wide substrate spectrum. The Δ g306 mutants were more sensitive to chemical stressors than the wild type. Disruption of g306 impeded the nematocidal efficiency of A. oligospora . Metabolomics analysis showed that secondary metabolite biosynthesis and lipid metabolism were altered in the mutants. The phenotypic changes in the mutants can be attributed to the down-regulation of various metabolites, including fatty acyls, prenol lipids, steroidsand steroid derivative, and amino acid derivatives, identified in the present study. This study investigated the association between the non-ribosomal polypeptide-encoding gene g306 and nematicidal activity in A. oligospora , providing a reference for resolving the predation mechanism of nematode-trapping fungus., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Gu, Lu, Liu, Zhang and Wang.)

This study investigated the effects of SIRT1 gene knock-out on osteoarthritis in mice, and the possible roles of SREBP2 protein and the PI3K/AKT signaling pathway in the effects. Mice were randomly divided into a normal group and a SIRT1 gene knock-out group (6 mice in each group). In these groups, one side of the knee anterior cruciate ligament was traversed, and the ipsilateral medial meniscus was cut to establish an osteoarthritis model of knee joint. The countralateral synovial bursa was cut out, serving as controls. The knee joint specimens were then divided into four groups: SIRT1 control group (group A, n=6); SIRT1 osteoarthritis group (group B, n=6); SIRT1 control group (group C, n=6); SIRT1 osteoarthritis group (group D, n=6). HE staining, Masson staining, Safranin O-Fast Green staining and Van Gieson staining were used to observe the morphological changes in the articular cartilage of the knee. Immunohistochemical staining was employed to detect the expression of SIRT1, SREBP2, VEGF, AKT, HMGCR and type II collagen proteins. SA-β-gal staining was utilized to evaluate chondrocyte aging. The results showed clear knee joint cartilage destruction and degeneration in the SIRT1 osteoarthritis group. The tidal line was twisted and displaced anteriorly. Type II collagen was destroyed and distributed unevenly. Compared with the SIRT1 osteoarthritis group and SIRT1 control group, SIRT1 protein expression was not obviously changed in the SIRT1 osteoarthritis group ( P>0.05), while the expression levels of the SREBP2, VEGF and HMGCR proteins were significantly increased ( P<0.05) and the levels of AKT and type II collagen proteins were significantly decreased (P<0.05). SIRT1 gene knock-out may aggravate cartilage degeneration in osteoarthritis by activating the SREBP2 protein-mediated PI3K/AKT signalling pathway, suggesting that SIRT1 gene may play a protective role against osteoarthritis. [ABSTRACT FROM AUTHOR]

Background: CRISPR-Cas9 genome editing and labeling has emerged as an important tool in biologic research, particularly in regards to potential transgenic and gene therapy applications. Delivery of CRISPR-Cas9 plasmids to target cells is typically done by non-viral methods (chemical, physical, and/or electrical), which are limited by low transfection efficiencies or with viral vectors, which are limited by safety and restricted volume size. In this work, a non-viral transfection technology, named lance array nanoinjection (LAN), utilizes a microfabricated silicon chip to physically and electrically deliver genetic material to large numbers of target cells. To demonstrate its utility, we used the CRISPR-Cas9 system to edit the genome of isogenic cells. Two variables related to the LAN process were tested which include the magnitude of current used during plasmid attraction to the silicon lance array (1.5, 4.5, or 6.0 mA) and the number of times cells were injected (one or three times). Results: Results indicate that most successful genome editing occurred after injecting three times at a current control setting of 4.5 mA, reaching a median level of 93.77 % modification. Furthermore, we found that genome editing using LAN follows a non-linear injection-dose response, meaning samples injected three times had modification rates as high as nearly 12 times analogously treated single injected samples. Conclusions: These findings demonstrate the LAN's ability to deliver genetic material to cells and indicate that successful alteration of the genome is influenced by a serial injection method as well as the electrical current settings. [ABSTRACT FROM AUTHOR]

We have constructed two plasmids that can be used for cloning as templates for PCR- -based gene disruption, mutagenesis and the construction of DNA chromosome translocation cassett es. To our knowledge, these plasmids are the fi rst vectors that confer resistance to ampicillin, kanamycin and hygromycin B in bacteria, and to geneticin (G418) and hygromycin B in Saccharomyces cerevisiae simultaneously. The option of simultaneously using up to three resistance markers provides a highly stringent control of recombinant selection and the almost complete elimination of background resistance, while unique restriction sites allow easy cloning of chosen genetic material. Moreover, we successfully used these new vectors as PCR templates for the induction of chromosome translocation in budding yeast by the bridge-induced translocation system. Cells in which translocation was induced carried chromosomal rearrangements as expected and exhibited resistance to both, G418 and hygromycin B. These features make our constructs very handy tools for many molecular biology applications. [ABSTRACT FROM AUTHOR]

Members of the genus Ranavirus (family Iridoviridae ) are large double-stranded (ds) DNA viruses that are found world-wide infecting fish, amphibian and reptile ectothermic hosts. Ranavirus genomes range from 105 to 155 kbp in length and they are predicted to encode around 90–125 genes. Currently, our knowledge of the function of ∼50% of these genes is known or inferred based on homology to orthologous genes characterized in other systems; however, the function of the remaining open reading frames (ORFS) is unknown. Therefore, in order to begin to uncover the function of unknown ORFs in ranaviruses we developed a standardized approach to generate a recombination cassette for any ORF in Ambystoma tigrinum virus (ATV). Our standardized approach quickly and efficiently assembles recombination cassettes and recombinant ATV. We have used this approach to identify two essential, one semi-essential and two non-essential genes in ATV. [ABSTRACT FROM AUTHOR]

Hepatocarcinoma animal models, such as the induced tumor model, transplanted tumor model, gene animal model, are significant experimental tools for the evaluation of targeting drug delivery system as well as the pre-clinical studies of liver cancer. The application of antitumor drug-targeting models not only furnishes similar biological characteristics to human liver cancer but also offers guarantee of pharmacokinetic indicators of the liver-targeting preparations. In this article, we have reviewed some kinds of antitumor drug-targeting models of hepatoma and speculated that the research on this field would be capable of attaining a deeper level and expecting a superior achievement in the future. [ABSTRACT FROM PUBLISHER]

Objective To investigate the effect of SIRT1 gene knock-out on VEGF/AKT pathway in osteoarthritis mice, and to explore its role in the pathogenesis of cartilage degeneration in osteoarthritis. Methods The mice were divided into 2 groups: SIRT1 + / + mice osteoarthritis group （Group A, n = 6） and SIRT1- /- mice osteoarthritis group （Group B, n = 6）. FQ-PCR was used to detect the mRNA expression of SIRT1. HE staining and Safranin O-Fast Green staining were used to observe the morphological changes of the articular cartilage of the knee. The Mankin's score was used to evaluate the degree of articular cartilage degeneration. Immunohistochemical staining was used to detect the protein expressions of SIRT1, VEGF, and AKT. Results The mRNA expression of SIRT1 in Group B was 2. 24417 ± 1. 316569, which was significantly lower than that in Group A （P < 0. 01）. The HE staining and Safranin O-Fast Green staining showed that the articular cartilage in Group B degenerated obviously, with Mankin's score of 9. 8333 ± 1. 94079, which was significantly higher than that in Group A （P < 0. 05）. The immunohistochemical staining integrals of SIRT1,VEGF, and AKT in Group B were 3. 3333 ± 1. 96638, 10. 0000 ± 2. 44949, and 1. 3333 ± 1. 21106. The protein expression of SIRT1 in Group B was not significantly different from that in Group A （P > 0. 05）. The protein expression of VEGF in Group B was significantly higher than that in Group A （P < 0. 05）, but the protein expression of AKT in Group B was much lower than that in Group A （P < 0. 01）. Conclusion Knocking-out SIRT1 may aggravate cartilage degeneration in osteoarthritis through VEGF/AKT signal pathway activation. Therefore, SIRT1 may play a protective role against osteoarthritis. [ABSTRACT FROM AUTHOR]

Obesity is on the rise in westernized countries, and visceral obesity in particular is associated with enhanced risk of developing metabolic disease and accelerated aging. Various dietary restriction regimens have been shown to extend healthy lifespan in a variety of species. However, identification of alternative approaches that could be more acceptable to humans is actively being pursued. We have shown previously that mice deficient in pregnancy-associated plasma protein-A (PAPP-A) have an extended healthy lifespan on a regular chow diet. In this study, we determined the lifespan of PAPP-A knock-out (KO) and wild-type (WT) littermates fed a high fat diet (HFD) starting at 12 months of age. PAPP-A KO and WT mice had equivalent weight gain as measured over 25 weeks on HFD. However, PAPP-A KO mice on HFD had a significant increase in lifespan ( P = 0.018). Body composition and tissue pathology were assessed in a separate cohort of mice after 30 weeks on HFD. Percent body fat was equivalent in the two groups. However, there was a decrease in visceral fat depot weights and an increase in serum adiponectin levels in PAPP-A KO compared to WT mice. Major pathological differences were seen in kidney, heart and testes, with PAPP-A KO mice having little, if any, evidence of inflammation, mineralization, or degeneration in these tissues compared to WT mice. Thus, PAPP-A is a novel drug target with the potential to promote healthy longevity without a need for dietary restriction. [ABSTRACT FROM AUTHOR]

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Comamonas testosteroni ( C. testosteroni ) is a gram negative bacterium which can use steroid as a carbon source and degrade steroid with about 20 special enzymes. Most of the enzymes are inducible enzymes. 3-Oxoacyl-ACP reductase (E.C. 1.1.1.100) alternatively known as β-ketoacyl-ACP reductase (BKR) is involved in fatty acid syntheses. DNA sequence comparison showed that BKR belongs to the short-chain alcohol dehydrogenase (SDR) family. Our results showed that BKR is necessary for the degradation of steroid hormones in C. testosteroni . The DNA fragment of the BKR gene was cloned into an expressional plasmid pET-15b. BKR protein was expressed with 6× His-tag on the N-terminus and the enzyme was purified with Ni-column. Antibodies against BKR were prepared and a new BKR quantitative ELISA was created in our laboratory. The purified BKR is a 30.6 kDa protein on SDS–PAGE. C. testosteroni was induced by testosterone, estradiol, estriol and cholesterol. The expression of BKR was detected with an ELISA. The result showed that the BKR expression could be induced by cholesterol and estriol but not by testosterone and estradiol. BKR gene knock-out mutant (M-C.T.) was prepared by homologous integration. High performance liquid chromatography (HPLC) was used to detect steroid hormone degradation in C. testosteroni ATCC11996 and BKR gene knock-out mutant. We proved that the M-C.T. eliminated of testosterone degradation. Degradations of cholesterol and estradiol were also decreased. We conclude that the novel BKR in C. testosteroni plays an important role in steroid degradation. This work provides some new information of SDR and steroid degradation in C. testosteroni . [ABSTRACT FROM AUTHOR]

Bacillus amyloliquefaciens is an important industrial microorganism, which can be applied as a protein expression host. However, the extracellular protein expression ability of B. amyloliquefaciens is still low. Hence, it is necessary to develop a B. amyloliquefaciens host with a high extracellular protein expression capacity. In this study, B. amyloliquefaciens HZ-12 was the original strain, then seven important extracellular protease genes (epr , nprE , aprE -a, mpr , pbpF , vpr , ykct 1), one important intracellular protease gene (aprX) and two redundant proteins genes (htrB , hag) were deleted in HZ-12, resulting in B. amyloliquefaciens BAX-10. In order to evaluate the extracellular protein expression ability of BAX-10, the alkaline protease gene aprE from Bacillus subtilis D7 was expressed in BAX-10. After fermentation, the alkaline protease activity of BAX-10/ aprE reached 666.82 U/mL, which was 57% higher than that of the control strain HZ/ aprE. Moreover, the deletion of the ten genes had no negative effect on the growth of B. amyloliquefaciens. In summary, B. amyloliquefaciens BAX-10 could be used as a potential platform host for expression of target extracellular proteins. • amyloliquefaciens with a high extracellular protease expression ability was constructed. • Neutral protease and alkaline protease were the main extracellular proteases of HZ12. • The alkaline protease activity of BAX-10/ aprE was 1.57 times than that of HZ/ aprE. • The alkaline protease expression ability of BAX-10/ aprE was higher than that of BL9/ aprE. [ABSTRACT FROM AUTHOR]

Lactococcus lactis-a food-grade nonpathogenic lactic acid bacterium-is used widely in the food industry. In this report, we describe an approach to construct deficient strains in L. lactis utilizing the λ-Red recombination system. Three kinds of recombinant proteins, λ exonuclease, β protein and γ protein, were induced by l-arabinose in L. lactis MG1363 harboring the plasmid pKD46. A chloramphenicol-resistant cassette was amplified from pGj103 containing homology arms of 50 nt to the thyA gene. The PCR-generated DNA fragment was then electroporated into L. lactis MG1363, which expressed the recombination proteins. ThyA-null strains resistant to chloramphenicol were obtained and their growth characteristics were analyzed in relation to thymidine requirement. The results revealed that the thyA gene in L. lactis MG1363 was successfully knocked out. This is the first time that the Red system has been used in a Gram-positive bacterium, and use of the techniques presented here should prompt rapid and efficient mutagenesis or modification of L. Lactis chromosomal genes. [ABSTRACT FROM AUTHOR]

Abstract: Trypanosoma cruzi calreticulin (TcCRT) can hijack complement C1, mannan-binding lectin and ficolins from serum thus inhibiting the classical and lectin complement pathway activation respectively. To understand the in vivo biological functions of TcCRT in T. cruzi we generated a clonal cell line lacking one TcCRT allele (TcCRT+/−) and another clone overexpressing it (TcCRT+). Both clones were derived from the TCC T. cruzi strain. As expected, TcCRT+/− epimastigotes showed impairment on TcCRT synthesis, whereas TcCRT+ ones showed increased protein levels. In correlation to this, monoallelic mutant parasites were significantly susceptible to killing by the complement machinery. On the contrary, TcCRT+ parasites showed higher levels of resistance to killing mediate by the classical and lectin but not the alternative pathway. The involvement of surface TcCRT in depleting C1 was demonstrated through restoration of serum killing activity by addition of exogenous C1. In axenic cultures, a reduced propagation rate of TcCRT+/− parasites was observed. Moreover, TcCRT+/− parasites presented a reduced rate of differentiation in in vitro assays. As shown by down- or upregulation of TcCRT expression this gene seems to play a major role in providing T. cruzi with the ability to resist complement system. [Copyright &y& Elsevier]

Open reading frame 17 ( Bm17) gene of Bombyx mori nucleopolyhedrovirus is a highly conserved gene in lepidopteran nucleopolyhedroviruses, but its function remains unknown. In this report, transient-expression and superinfection assays indicated that BM17 localized in the nucleus and cytoplasm of infected BmN cells. To determine the role of Bm17 in baculovirus life cycle, we constructed a Bm17 knockout virus and characterized its properties in cells. Analysis of the production and infection of budded virions, the level of viral DNA replication revealed showed that there was no significant difference among the mutant, the control, and the Bm17 repaired virus strains. These results suggest that BM17 is not essential for virus replication in cultured cells. [ABSTRACT FROM AUTHOR]

Background: NUAK1 and NUAK2, members of the AMP-activated protein kinase family of serine/threonine kinases, are prominently expressed in neuroectoderm, but their functions in neurulation have not been elucidated. Results: NUAK1 and NUAK2 double mutants exhibited exencephaly, facial clefting, and spina bifida. Median hinge point was formed, but dorsolateral hinge point formation was not apparent in cranial neural plate; neither apical constriction nor apico-basal elongation took place efficiently in the double mutants during the 5-10-somite stages. Concomitantly, the apical concentration of phosphorylated myosin light chain 2, F-actin, and cortactin was insignificant, and development of acetylated α-tubulin-positive microtubules was poor. However, the distribution of F-actin, cortactin, Shroom3, Rho, myosin heavy chain IIB, phosphorylated myosin light chain 2, α-tubulin, γ-tubulin, or acetylated α-tubulin was apparently normal in the double mutant neuroepithelia at the 5-somite stage. Conclusions: NUAK1 and NUAK2 complementarily function in the apical constriction and apico-basal elongation that associate with the dorsolateral hinge point formation in cephalic neural plate during the 5- to 10-somite stages. In the double mutant neural plate, phosphorylated myosin light chain 2, F-actin, and cortactin did not concentrate efficiently in apical surfaces, and acetylated α-tubulin-positive microtubules did not develop significantly. Developmental Dynamics 241:1350-1364, 2012. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Zinc-finger nucleases ( ZFNs) are artificial enzymes that create site-specific double-strand breaks and thereby induce targeted genome editing. Here, we demonstrated successful gene disruption in somatic and germ cells of medaka ( Oryzias latipes) using ZFN to target exogenous EGFP genes. Embryos that were injected with an RNA sequence pair coding for ZFNs showed mosaic loss of green fluorescent protein fluorescence in skeletal muscle. A number of mutations that included both deletions and insertions were identified within the ZFN target site in each embryo, whereas no mutations were found at the non-targeted sites. In addition, ZFN-induced mutations were introduced in germ cells and efficiently transmitted to the next generation. The mutation frequency varied (6-100%) in the germ cells from each founder, and a founder carried more than two types of mutation in germ cells. Our results have introduced the possibility of targeted gene disruption and reverse genetics in medaka. [ABSTRACT FROM AUTHOR]

Over the past 25 years, the reverse genetic approach including precise and conditional replacement or loss of gene function at a specific locus was considered possible only in mice due to the absence of embryonic stem (ES) or induced pluripotent stem (iPS) cell lines in other species. Recently, however, stem cell technology in rats has become available for biomedical research. In this paper we overview the recent progress of rat ES and iPS cell technology. Starting from the establishment of rat ES cells, the use of ES cells for foreign gene transfer and endogenous gene knock-out is discussed, followed by the successful establishment of rat iPS cells and the generation of an iPS cell-derived organ via interspecific blastocyst complementation. Finally, the possible contribution of rat stem cell technology to reproductive medicine is described. [ABSTRACT FROM AUTHOR]

Abstract: Phosphoinositide-specific phospholipase C (PI-PLC) is a major regulator of calcium-dependent signal transduction, which has been shown to be important in various processes of the malaria parasite Plasmodium. PI-PLC is generally implicated in calcium liberation from intracellular stores through the action of its product, inositol-(1,4,5)-trisphosphate, and is itself dependent on calcium for its activation. Here we describe the plc genes from Plasmodium species. The encoded proteins contain all domains typically found in PI-PLCs of the δ class but are almost twice as long as their orthologues in mammals. Transcriptional analysis by qRT-PCR of plc during the erythrocytic cycle of P. falciparum revealed steady expression levels that increased at the late schizont stages. Genetic analysis in the P. berghei model revealed that the plc locus was targetable but that plc gene knock-outs could not be obtained, thereby strongly indicating that the gene is essential during blood stage development. Alternatively, we attempted to modify plc expression through a promoter exchange approach but found the gene to be refractory to over-expression indicating that plc expression levels might additionally be tightly controlled. [Copyright &y& Elsevier]

Abstract: Hydroperoxide detoxification in African trypanosomes is achieved by 2-Cys-peroxiredoxin (TXNPx)- and non-selenium glutathione peroxidase (Px)-type enzymes which both obtain their reducing equivalents from the unique trypanothione/tryparedoxin system. Previous RNA interference approaches revealed that the cytosolic TXNPx and the Px-type enzymes are essential for Trypanosoma brucei. Because of partially overlapping in vitro substrate specificities and subcellular localisation the physiological function of the individual enzymes was not yet clear. As shown here, TXNPx and Px are expressed at comparable levels and in their active reduced state. Px-overexpressing parasites were less sensitive toward linoleic acid hydroperoxide but not hydrogen peroxide. Kinetic studies confirmed that Px—but not TXNPx—reduces lipophilic hydroperoxides including phospholipids with high efficiency. Most interestingly, the severe proliferation defect of Px-depleted bloodstream cells could be rescued by Trolox, but not by hydrophilic antioxidants, in the medium. This allowed us to knock-out the three Px genes individually and thus to distinguish their in vivo role. Deletion of the cytosolic Px I and II resulted in extremely fast membrane peroxidation followed by cell lysis. Cells lacking specifically the mitochondrial Px III showed a transient growth retardation and cardiolipin peroxidation but adapted within 24h to normal proliferation. [Copyright &y& Elsevier]

The calY gene, encoding metalloprotease camelysin in the Bacillus thuringiensis acrystalliferous strain XBU001, was amplified and sequenced. The camelysin from the calY sequence was 199 amino acids in size ( c. 22 000 Da). The temperature-sensitive plasmid pKESX was used to construct a metalloprotease camelysin-deficient strain of B. thuringiensis. The calY gene was replaced by an erythromycin-resistant gene in KCTF. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and MS analysis showed that the metalloprotease InhA was not expressed after knocking out the gene calY. The temperature-sensitive plasmid pKPC was used to construct a metalloprotease camelysin complementation strain KCTFC. The InhA protein was found in KCTFC. Analysis of the expression of InhA in the wild-type strain KCTF12, camelysin-deficient and complementation strains indicated that inhA expression depended on camelysin. Although camelysin did not directly regulate the expression of the InhA through binding to the promoter of the inhA, the results suggest that camelysin can positively regulate the expression of the InhA protein. [ABSTRACT FROM AUTHOR]

Extensive biochemical and structural analyses have been performed on the putative DNA repair proteins of hyperthermophilic archaea, in contrast to the few genetic analyses of the genes encoding these proteins. Accordingly, little is known about the repair pathways used by archaeal cells at high temperature. Here, we attempted to disrupt the genes encoding the potential repair proteins in the genome of the hyperthermophilic archaeon Thermococcus kodakaraensis. We succeeded in isolating null mutants of the hjc, hef, hjm, xpb, and xpd genes, but not the radA, rad50, mre11, herA, nurA, and xpg/fen1genes. Phenotypic analyses of the gene-disrupted strains showed that the xpb and xpd null mutants are only slightly sensitive to ultraviolet (UV) irradiation, methyl methanesulfonate (MMS) and mitomycin C (MMC), as compared with the wild-type strain. The hjm null mutant showed sensitivity specifically to mitomycin C. On the other hand, the null mutants of the hjc gene lacked increasing sensitivity to any type of DNA damage. The Hef protein is particularly important for maintaining genome homeostasis, by functioning in the repair of a wide variety of DNA damage in T. kodakaraensis cells. Deletion of the entire hef gene or of the segments encoding either its nuclease or helicase domain produced similar phenotypes. The high sensitivity of the Δhef mutants to MMC suggests that Hef performs a critical function in the repair process of DNA interstrand cross-links. These damage-sensitivity profiles suggest that the archaeal DNA repair system has processes depending on repair-related proteins different from those of eukaryotic and bacterial DNA repair systems using homologous repair proteins analyzed here. [ABSTRACT FROM AUTHOR]

Abstract: The industrially applied ascomycete Hypocrea jecorina (synonym: Trichoderma reesei) exhibits a low rate of exogenous DNA integration by homologous recombination (HR). This hinders the high-throughput generation of strains by gene replacement and is therefore impeding systematic functional gene analyses towards, e.g. strain improvement for protein or enzyme production. To increase the rate of HR events during fungal transformation we identified and deleted the orthologue of the human KU70 in H. jecorina, which is required for the nonhomologous end joining (NHEJ) pathway and responsible for ectopic DNA integration. The effect of the absence of the H. jecorina tku70 on gene targeting was tested by deletion of two so far uncharacterized genes encoding a short chain dehydrogenase and a fungal specific transcription factor. Efficiency of gene targeting for both genes was >95% in a Δtku70 strain when 1kb homologous flanking regions were used in the deletion construct. This is a significant increase in targeting efficiency compared to the parental – non-tku70 deleted – strain TU-6 where a gene knock-out frequency of only 5–10% was observed. Together with the recently annotated genomic sequence of H. jecorina, this system provides a useful tool for a genome-wide functional gene analysis on a high-throughput scale to improve the biotechnological potential of this fungus. [Copyright &y& Elsevier]

AXL, a member of the TAM family, is a promising therapeutic target due to its elevated expression in advanced hepatocellular carcinoma (HCC), particularly in association with acquired drug resistance. Previously, RNA interference was used to study its role in cancer, and several phenotypic changes, including attenuated cell proliferation and decreased migration and invasion, have been reported. The mechanism of action of AXL in HCC is elusive. We first studied the AXL expression in HCC cell lines by real-time PCR and western blot and showed its stringent association with a mesenchymal phenotype. We then explored the role of AXL in mesenchymal SNU475 cells by CRISPR-Cas9 mediated gene knock-out. AXL-depleted HCC cells displayed drastic phenotypic changes, including increased DNA damage response, prolongation of doubling time, G2 arrest, and polyploidization in vitro and loss of tumorigenicity in vivo. Pharmacological inhibition of AXL by R428 recapitulated G2 arrest and polyploidy phenotype. These observations strongly suggest that acute loss of AXL in some mesenchymal HCC cells is lethal and points out that its inhibition may represent a druggable vulnerability in AXL-high HCC patients. [ABSTRACT FROM AUTHOR]

Abstract: Mycothiol (1d-myo-inosityl 2-[N-acetyl-l-cysteinyl]amido-2-deoxy-α-d-glucopyranoside) is an important microbial thiol present only in actinomycetes. Rhodococcus jostii RHA1 degrades a wide range of xenobiotics, including polychlorinated biphenyls, nitriles and N-nitrosodimethylamine. Analyses revealed that this strain produces two thiols, mycothiol and ergothioneine, found in the other actinomycetes. A mycothiol ligase mutant strain of R. jostii RHA1 deficient in the production of mycothiol was constructed. This mutant has a number of interesting characteristics: (a) it overproduces the intermediate glucosamine-inositol (1-O-(2-amino-1-deoxy-α-d-glucopyranosyl)-d-myo-inositol); (b) it is deficient in the biochemical degradation of a number of xenobiotics metabolized by the parent strain; (c) it shows increased susceptibility to a number of antibiotics; and (d) it shows unusual growth characteristics, exhibiting a long lag phase before normal exponential growth. The diverse phenotypes of the mutant indicate the utility of R. jostii RHA1 as a model for deciphering the various functions of mycothiol. [Copyright &y& Elsevier]

Abstract: The role of wiring molecules in circuit assembly is tested directly in genetically engineered animals, in which the corresponding gene has been selectively mutated. Minor alterations in neuronal circuits in these mutant animals are explained by redundancy and/or adaptive changes of other genes relevant for brain development. There is very little known, however, about the extent and nature of the compensatory molecular mechanisms. Using gene microarrays, we compared gene expression patterns in the somatosensory cortex of wild type and ephrinA5 deficient mice, which exhibit subtle, but highly reproducible alterations of thalamocortical projections and intrinsic cortical circuits. We found that between 2.2%–5.7% of all transcripts (140–373 targets) detected in the somatosensory cortex are differentially expressed in comparing wild type and ephrinA5 mutants. A gene group analysis of the annotated transcripts revealed that a high proportion of the dysregulated genes encode proteins relevant for circuit development. Finer grain analysis by in situ hybridization and quantitative RT-PCR revealed that 20% of the Eph/ephrin family genes expressed in the somatosensory cortex are up-regulated in the mutant. One of these genes, EphB6, was up-regulated in all cortical layers, where it is normally expressed. However, the ephrinA2 and EphA5 were up-regulated only in selected layers in the cortex of the mutant; expression levels in other layers did not change. These findings indicate that there is specificity of adaptive and compensative changes in gene expression after the mutation of a single gene relevant for cortical development. Our results also point to the complexity of interpreting phenotypes of gene knock-out animals. [Copyright &y& Elsevier]

Abstract: In many bacteria, gene replacement can only be achieved using RP4-based conjugative systems where exogenous DNA is delivered to the recipient on conditionally replicating plasmids carrying an oriT RP4. In the commonly used strains SM10 and S17-1 conjugative functions are provided by an RP4 plasmid inserted in the chromosome. Those strains, besides mobilizing oriT RP4-carrying plasmids, also transfer their own chromosomal genes, which can be inconvenient for several reasons. We describe here a new version of an RP4-based conjugative system that allows for efficient transfer of mobilizable plasmids without the transfer of chromosomal genes, providing fully controlled and efficient exogeneous DNA delivery to non-transformable bacteria. [Copyright &y& Elsevier]

Experience-dependent changes in the structure of dendritic spines may contribute to learning and memory. Encoded by three genes, the Shank family of postsynaptic scaffold proteins are abundant and enriched in the postsynaptic density (PSD) of central excitatory synapses. When expressed in cultured hippocampal neurons, Shank promotes the maturation and enlargement of dendritic spines. Recently, Shank3 has been genetically implicated in human autism, suggesting an important role for Shank proteins in normal cognitive development. Here, we report the phenotype of Shank1 knock-out mice. Shank1 mutants showed altered PSD protein composition; reduced size of dendritic spines; smaller, thinner PSDs; and weaker basal synaptic transmission. Standard measures of synaptic plasticity were normal. Behaviorally, they had increased anxiety-related behavior and impaired contextual fear memory. Remarkably, Shank1-deficient mice displayed enhanced performance in a spatial learning task; however, their long-term memory retention in this task was impaired. These results affirm the importance of Shank1 for synapse structure and function in vivo, and they highlight a differential role for Shank1 in specific cognitive processes, a feature that may be relevant to human autism spectrum disorders. [ABSTRACT FROM AUTHOR]

Abstract: To date, the function of MADS-domain transcription factors in non-seed plants remains largely elusive, although a number of genes have been isolated and characterized from a variety of species. In our study we analyzed PPM2, a classical MIKC-type MADS-box gene from the moss Physcomitrella patens, taking advantage of the unique technical properties Physcomitrella offers in terms of efficient homologous recombination. We determined mRNA and protein distribution and performed targeted disruption of the genomic locus for functional analysis of PPM2. Despite weak ubiquitous expression, PPM2 protein is mostly found in male and female gametangia and basal parts of developing sporophytes. Therefore, PPM2 seems to function in both the haploid and the diploid phase of the moss life cycle. This situation reflects an evolutionary transition state of gene recruitment from an ancestral gametophytic generation into a derived sporophytic generation which became dominating in tracheophytes. However, a knock-out of the PPM2 gene did not cause visible phenotypical changes in the respective structures. The implications of our findings for the understanding of the evolutionary history of MADS-box transcription factors in plants are discussed. [Copyright &y& Elsevier]

Abstract: In a previous study it was shown that a simple random Boolean network model, with two input connections per node, can describe with a good approximation (with the exception of the smallest avalanches) the distribution of perturbations in gene expression levels induced by the knock-out of single genes in Saccharomyces cerevisiae. Here we address the reason why such a simple model actually works: we present a theoretical study of the distribution of avalanches and show that, in the case of a Poissonian distribution of outgoing links, their distribution is determined by the value of the Derrida exponent. This explains why the simulations based on the simple model have been effective, in spite of the unrealistic hypothesis about the number of input connections per node. Moreover, we consider here the problem of the choice of an optimal threshold for binarizing continuous data, and we show that tuning its value provides an even better agreement between model and data, valuable also in the important case of the smallest avalanches. Finally, we also discuss the choice of an optimal value of the Derrida parameter in order to match the experimental distributions: our results indicate a value slightly below the critical value 1. [Copyright &y& Elsevier]

To better understand the role of multiple neurotrophin ligands and their receptors in vertebrate brain evolution, we examined the distribution of trk neurotrophin receptors in representatives of several vertebrate classes. Trk receptors are largely expressed in homologous neuronal populations among different species/classes of vertebrates. In many neurons, trkB and trkC receptors are co-expressed. TrkB and trkC receptors are primarily found in neurons with more restricted, specialized dendritic and axonal fields that are thought to be involved in discriminative or ‘analytical’ functions. The neurotrophin receptor trkA is expressed predominantly in neurons with larger, overlapping dendritic fields with more heterogeneous connections (‘integrative’ or ‘modulatory’ systems) such as nociceptive and sympathetic autonomic nervous system, locus coeruleus and cholinergic basal forebrain. Surveys of trk receptor expression and function in the peripheral nervous system of different vertebrate classes reveal trends ranging from dependency on a single neurotrophin to a more complex dependency on increasing numbers of neurotrophins and their receptors, for example, in taste and inner ear innervation. Gene deletion studies in mice provide evidence for a complex regulation of neuronal survival of sensory ganglion cells by different neurotrophins. Although expression of neurotrophins and their receptors is predominantly conserved in most circuits, increasing diversity of neurotrophin ligands and their receptors and a more complex dependency of neurons on neurotrophins might have facilitated the formation of at least some new neuronal entities. Copyright © 2006 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Myelin-forming oligodendrocytes facilitate saltatory nerve conduction and support neuronal functions in the mammalian CNS. Although the processes of oligodendrogliogenesis and differentiation from neural progenitor cells have come to light in recent years, the molecular mechanisms underlying oligodendrocyte myelinogenesis are poorly defined. Herein, we demonstrate the pivotal role of the basic helixloop-helix transcription factor, Olig1, in oligodendrocyte myelinogenesis in brain development. Mice lacking a functional Olig1 gene develop severe neurological deficits and die in the third postnatal week. In the brains of these mice, expression of myelin-specific genes is abolished, whereas the formation of oligodendrocyte progenitors is not affected. Furthermore, multilamellar wrapping of myelin membranes around axons does not occur, despite recognition and contact of axons by oligodendrocytes, and Olig1-null mice develop widespread progressive axonal degeneration and gliosis. In contrast, myelin sheaths are formed in the spinal cord, although the extent of myelination is severely reduced. At the molecular level, we find that Olig1 regulates transcription of the major mydin-specific genes, Mbp,Plp1, and Mag, and suppresses expression of a major astrocyte-specific gene, Gfap. Together, our data indicate that Olig1 is a central regulator of oligodendrocyte myelinogenesis in brain and that axonal recognition and myelination by oligodendrocytes are separable processes. [ABSTRACT FROM AUTHOR]

Mammillary bodies and the mammillothalamic tract are parts of a classic neural circuitry that has been implicated in severe memory disturbances accompanying Korsakoff's syndrome. However, the specific role of mammillary bodies in memory functions remains controversial, often being considered as just an extension of the hippocampal memory system. To study this issue we used mutant mice with a targeted mutation in the transcription factor geneFoxb1.These mice suffer perinatal degeneration of the medial and most of the lateral mammillary nuclei, as well as of the mammillothalamic bundle.Foxb1mutant mice showed no deficits in such hippocampal-dependent tasks as contextual fear conditioning and social transmission of food preference. They were also not impaired in the spatial reference memory test in the radial arm maze. However,Foxb1mutants showed deficits in the task for spatial navigation within the Barnes maze. Furthermore, they showed impairments in spatial working memory tasks such as the spontaneous alternation and the working memory test in the radial arm maze. Thus, our behavioural analysis ofFoxb1mutants suggests that the medial mammillary nuclei and mammillothalamic tract play a role in a specific subset of spatial tasks, which require combined use of both spatial and working memory functions. Therefore, the mammillary bodies and the mammillothalamic tract may form an important route through which the working memory circuitry receives spatial information from the hippocampus. [ABSTRACT FROM AUTHOR]

Vertebrate synapsins are abundant synaptic vesicle phosphoproteins that have been proposed to fine-regulate neurotransmitter release by phosphorylation-dependent control of synaptic vesicle motility. However, the consequences of a total lack of all synapsin isoforms due to a knock-out of all three mouse synapsin genes have not yet been investigated. In Drosophila a single synapsin gene encodes several isoforms and is expressed in most synaptic terminals. Thus the targeted deletion of the synapsin gene of Drosophila eliminates the possibility of functional knock-out complementation by other isoforms. Unexpectedly, synapsin null mutant flies show no obvious defects in brain morphology, and no striking qualitative changes in behaviour are observed. Ultrastructural analysis of an identified ‘model’ synapse of the larval nerve muscle preparation revealed no difference between wild-type and mutant, and spontaneous or evoked excitatory junction potentials at this synapse were normal up to a stimulus frequency of 5 Hz. However, when several behavioural responses were analysed quantitatively, specific differences between mutant and wild-type flies are noted. Adult locomotor activity, optomotor responses at high pattern velocities, wing beat frequency, and visual pattern preference are modified. Synapsin mutant flies show faster habituation of an olfactory jump response, enhanced ethanol tolerance, and significant defects in learning and memory as measured using three different paradigms. Larval behavioural defects are described in a separate paper. We conclude that Drosophila synapsins play a significant role in nervous system function, which is subtle at the cellular level but manifests itself in complex behaviour. [ABSTRACT FROM AUTHOR]

It is shown here how gene knock-out experiments can be simulated in Random Boolean Networks (RBN), which are well-known simplified models of genetic networks. The results of the simulations are presented and compared with those of actual experiments in S. cerevisiae. RBN with two incoming links per node have been considered, and the Boolean functions have been chosen at random among the set of so-called canalizing functions.Genes are knocked-out (i.e. silenced) one at a time, and the variations in the expression levels of the other genes, with respect to the unperturbed case, are considered. Two important variables are defined: (i) avalanches, which measure the size of the perturbation generated by knocking out a single gene, and (ii) susceptibilities, which measure how often the expression of a given gene is modified in these experiments.A remarkable observation is that the distributions of avalanches and susceptibilities are very robust, i.e. they are very similar in different random networks; this should be contrasted with the distribution of other variables that show a high variance in RBN.Moreover, the distribution of avalanches and susceptibilities of the RBN models are close to those observed in actual experiments performed with S. cerevisiae, where the changes in gene expression levels have been recorded with DNA microarrays.These findings suggest that these distributions might be “generic” properties, common to a wide range of genetic models and real genetic networks. The importance of such generic properties is discussed. [Copyright &y& Elsevier]

Histamine is a versatile mediator that, according to in vitro studies, affects the synthesis of inflammatory cytokines and acute-phase proteins. The histidine-decarboxylase knockout (HDC–/–) mouse is a model of in vivo investigation of the physiologic and metabolic integration of the acutephase response. These mice do not synthesise histamine and feeding them with histamine-poor diet they are almost completely histamine-deficient. We compared the serum concentrations of representatives of acute-phase plasma proteins, as well as the levels IL-6 and IL-1α in wild type and HDC–/– mice during local (turpentine-induced) or systemic (LPS-induced) inflammation. The level of some acute-phase proteins significantly differed in wild-type and HDC–/– mice while others remained unaffected. The IL-6 levels are also differ in the wild-type and histamine-deficient animals, suggesting that the effect of histamine is attained through IL-6, although direct effect is not disclosed yet. [ABSTRACT FROM AUTHOR]

Nigrostriatal dopaminergic neurons express many nicotinic acetylcholine receptor (nAChR) subunits capable of forming multiple nAChR subtypes. These subtypes are expressed differentially along the neuron and presumably mediate diverse responses. β3 subunit mRNA has restricted expression but is abundant in the substantia nigra and ventral tegmental areas. To investigate the potential tole(s) of nicotinic receptors containing the β3 subunit in dopaminergic tracts, we generated mice with a null mutation in the β3 gene. We were thereby able to identify a population of β3-dependent α-conotoxin MII-binding nAChRs that modulate striatal dopamine release. Changes were also observed in locomotor activity and prepulse inhibition of acoustic startle, behaviors that are controlled, in part, by nigrostriatal and mesolimbic dopaminergic activity, respectively, suggesting that β3-containing nAChRs modulate these behaviors. [ABSTRACT FROM AUTHOR]