Templated mutagenesis in bacteriophage T4 involving imperfect direct or indirect sequence repeats

Some mutations arise in association with a potential sequence donor that consists of an imperfect direct or reverse repeat. Many such mutations are complex; that is, they consist of multiple close sequence changes. Current models posit that the primer terminus of a replicating DNA molecule dissociates, reanneals with an ectopic template, extends briefly, and then returns to the cognate template, bringing with it a locally different sequence; alternatively, a hairpin structure may form the mutational intermediate when processed by mismatch repair. This process resembles replication repair, in which primer extension is blocked by a lesion in the template; in this case, the ectopic template is the other daughter strand, and the result is error-free bypass of the lesion. We previously showed that mutations that impair replication repair can enhance templated mutagenesis. We show here that the intensity of templated mutation can be exquisitely sensitive to its local sequence, that the donor and recipient arms of an imperfect inverse repeat can exchange roles, and that double mutants carrying two alleles, each affecting both templated mutagenesis and replication repair, can have unexpected phenotypes. We also record an instance in which the mutation rates at two particular sites change concordantly with a distant sequence change, but in a manner that appears unrelated to templated mutagenesis.     

Cytologic diagnosis of Bartholin's gland adenocarcinoma

An adenocarcinoma of Bartholin's gland was diagnosed by a smear of a swollen lesion of the left vulva, with confirmation on the subsequent surgical specimen. This appears to be the second such case in which the diagnosis was established by cytologic examination of the smear. This rare tumor should be considered in patients presenting with vulvar swellings; cytologic examination can be useful in its early diagnosis, as demonstrated by this case.     

Histological and molecular biology diagnosis of neurocysticercosis in a patient without history of travel to endemic areas – Case report

Background: in endemic areas, neurocysticercosis appears mainly as a single, large, spherical and non-enhancing intracranial cyst. Case presentation: an atypical case of neurocysticercosis (NCC) in a French Caucasian, without history of travel to endemic areas, was confirmed by histology and molecular speciation. Imaging was atypical, showing several hook-bearing scolices visible in the cyst, while the serology employed was non-contributary. Conclusions: NCC should be considered when multiple taeniid scolices are observed within the same cystic lesion.     

Genetic control of susceptibility to mite-associated ulcerative dermatitis

Variable susceptibility to mite-associated ulcerative dermatitis (MAUD) attributable to Myobia musculi infestation was studied in breeding stocks of sixteen inbred strains of mice. Statistical evaluation of 41 occurrences of lesion among 1,517 mice of the various strains indicated that significant differences in the frequency of MAUD were associated with differences in genetic background and in the H-2 type. These findings suggest that the occurrence of an ulcerative skin lesion in inbred mice exposed to M. musculi is controlled by at least two genes. Lesion susceptibility appears to be profoundly affected by a non-H-2 linked gene or gene combination shared by all C57Bl background strains. In addition, a major influence is exerted by one or more genes within the H-2 complex.     

Nasal bone hemangiomas: a review of clinical, radiologic, and operative experience

A case of hemangioma of the nasal bones is reported. Clinical and radiologic findings, including CT scan, are presented and the literature reviewed. Although rare, the lesion often has a characteristic clinical and radiologic presentation that can be recognized preoperatively. CT scanning is helpful in defining tumor characteristics and extent. Surgery appears curative in most cases without significant disfigurement. For smaller lesions, bone graft of the defect appears unnecessary and the presence of intact periosteum may actually contribute to regeneration of normal bone.     

Electron microscopic study of (A)BC excinuclease. DNA is sharply bent in the UvrB-DNA complex.

Nucleotide excision repair in Escherichia coli is initiated by the UvrA, UvrB and UvrC proteins. UvrA is the damage recognition subunit, makes an A2B1 complex with the targeting subunit UvrB, and the complex binds to the lesion site; UvrA dissociates leaving behind a very stable UvrB-DNA complex that is recognized by the trigger subunit, UvrC, and the ensuing UvrB-UvrC heterodimer makes two incisions, one on either side of the lesion. Using electron microscopy, we investigated the structures of these early A, A-B intermediates on DNA containing ultraviolet light photoproducts. UvrA, which is known to bind to DNA as a dimer and produce a DNase I footprint of 33 base-pairs does not change the trajectory of DNA appreciably. The A2B1 complex clearly shows a bipartite structure and its effect on the trajectory of the DNA was not consistently straight or kinked. In contrast, the DNA in the preincision UvrB-DNA complex appears to be severely kinked; 43% of the molecules are bent by 80 degrees or more, with an average bending angle of 127 degrees. It appears that protein-induced bending is an important step on the pathway leading to excision of the damaged nucleotide by (A)BC excinuclease.     

Phaeohyphomicosis by Wangiella dermatitidis in Republic Argentine.

We are presenting the case of a 54 year-old woman, who had a kidney transplant. She came to our laboratory to consult for two cutaneous lesions: a cystic one at the back of her right leg and one localized on dorsum of left forearm. Biopsies of both lesions were performed for a histopathologic study as well as microbiological (both bacteriologic and mycologic) cultures. The histopathologic study showed a lesion compatible with a B type cutaneous lymphoma in the lesion in her leg, while in the mycologic study of the cystic lesion elements compatible with phaeohyphomycosis were observed. Development of Wangiella dermatitidis was obtained in the cultures. The cystic lesion localized on forearm was completely removed by surgery, while the lesion in the leg received oncological treatment. The aim of this paper is to describe the first published case of phaeohyphomycosis, by W. dermatitidis, in the Argentine Republic.     

Calcifying odontogenic cyst--Gorlin's cyst--report of two cases

The authors present two cases of calcifying odontogenic cysts, which were confirmed by histological examination. In the first case the radiographic findings and clinical status did not indicate the presence of a calcifying odontogenic cyst. In the second case, differential diagnosis included COC. The histopathological findings showed that what appeared to be simple cases of bone translucencies was in fact an unusual odontogenic lesion. The two cases point out the possibility of incorrect assessment of deceptively banal cases in daily specialist practice.     

A porphyrin pathway impairment is responsible for the phenotype of a dominant disease lesion mimic mutant of maize.

The maize lesion mimic gene Les22 is defined by dominant mutations and characterized by the production of minute necrotic spots on leaves in a developmentally specified and light-dependent manner. Phenotypically, Les22 lesions resemble those that are triggered during a hypersensitive disease resistance response of plants to pathogens. We have cloned Les22 by using a Mutator-tagging technique. It encodes uroporphyrinogen decarboxylase (UROD), a key enzyme in the biosynthetic pathway of chlorophyll and heme in plants. Urod mutations in humans are also dominant and cause the metabolic disorder porphyria, which manifests itself as light-induced skin morbidity resulting from an excessive accumulation of photoexcitable uroporphyrin. The phenotypic and genetic similarities between porphyria and Les22 along with our observation that Les22 is also associated with an accumulation of uroporphyrin revealed what appears to be a case of natural porphyria in plants.     

Phialophora verrucosa-induced subcutaneous phaeohyphomycosis. Fine needle aspiration findings

A 34-year-old woman on immunosuppressive therapy presented with a subcutaneous, cystic lesion on the dorsum of the right foot. Cytologic examination of material obtained by fine needle aspiration (FNA) revealed a mixture of acute and granulomatous inflammation as well as brown-pigmented fungi in the form of budding yeast, pseudohyphae and septate hyphae. The findings suggested subcutaneous phaeohyphomycosis (phaeomycotic cyst). Culture grew Phialophora verrucosa. The cytologic, histologic and cultural findings are given. This case demonstrates that phaeohyphomycosis can be diagnosed by FNA but that fungal culture is necessary to establish the identity of the etiologic agent. This appears to be the first case of P. verrucosa-induced subcutaneous phaeohyphomycosis reported in the Western Hemisphere.     

DNA lesion bypass polymerases open up

Structures of catalytic fragments of two DNA lesion bypass DNA polymerases, yeast DNA polymerase eta and an archeon DinB homolog, have recently been solved. These structures share several common architectural and structural features observed in other DNA polymerases, including a hand-like architecture with fingers, palm, and thumb subdomains. The new structures provide the first structural insights into DNA lesion bypass. The fingers and thumb are smaller than those in other DNA polymerases. Modeled substrates suggest that the fingers in the vicinity of the incoming nucleotide is closed, a conformation not previously observed for an unliganded polymerase. However, the template binding pocket appears to be more open, indicating that for DNA polymerase eta, a covalently linked thymine-thymine dimer could be accommodated.     

Synthesis in vitro of precursors of the catalytic subunits of acetylcholinesterase from Torpedo marmorata and Electrophorus electricus

We translated poly(A-rich messenger RNA prepared from the electric organs of Electrophorus electricus and Torpedo marmorata in a reticulocyte lysate system. In the case of Electrophorus, which appears to contain only one type of acetylcholinesterase catalytic subunit, an anti-(Electrophorus acetylcholinesterase) antiserum precipitated a single 65-kDa polypeptide from the products translation obtained in vitro. In the case of Torpedo, where a number of distinct catalytic subunits corresponding to different fractions of the enzyme have been described, an anti-(Torpedo acetylcholinesterase) antiserum precipitated two main polypeptides, 61 kDa and 65 kDa, both of which could be displaced by unlabelled purified Torpedo acetylcholinesterase. Synthesis in vitro thus appears to produce a single type of precursor of the acetylcholinesterase catalytic subunit for Electrophorus, and at least two distinct precursors for Torpedo, suggesting that several mRNAs code for the catalytic subunits in the latter species.     

Identification of pathways controlling DNA damage induced mutation in Saccharomyces cerevisiae

Mutation in response to most types of DNA damage is thought to be mediated by the error-prone sub-branch of post-replication repair and the associated translesion synthesis polymerases. To further understand the mutagenic response to DNA damage, we screened a collection of 4848 haploid gene deletion strains of Saccharomyces cerevisiae for decreased damage-induced mutation of the CAN1 gene. Through extensive quantitative validation of the strains identified by the screen, we identified ten genes, which included error-prone post-replication repair genes known to be involved in induced mutation, as well as two additional genes, FYV6 and RNR4. We demonstrate that FYV6 and RNR4 are epistatic with respect to induced mutation, and that they function, at least partially, independently of post-replication repair. This pathway of induced mutation appears to be mediated by an increase in dNTP levels that facilitates lesion bypass by the replicative polymerase Pol delta, and it is as important as error-prone post-replication repair in the case of UV- and MMS-induced mutation, but solely responsible for EMS-induced mutation. We show that Rnr4/Pol delta-induced mutation is efficiently inhibited by hydroxyurea, a small molecule inhibitor of ribonucleotide reductase, suggesting that if similar pathways exist in human cells, intervention in some forms of mutation may be possible.     

The zero exemplar distance problem

Given two genomes with duplicate genes, Zero Exemplar Distance is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome. Blin, Fertin, Sikora, and Vialette recently proved that Zero Exemplar Distance for monochromosomal genomes is NP-hard even if each gene appears at most two times in each genome, thereby settling an important open question on genome rearrangement in the exemplar model. In this article, we give a very simple alternative proof of this result. We also study the problem Zero Exemplar Distance for multichromosomal genomes without gene order, and prove the analogous result that it is also NP-hard even if each gene appears at most two times in each genome. For the positive direction, we show that both variants of Zero Exemplar Distance admit polynomial-time algorithms if each gene appears exactly once in one genome and at least once in the other genome. In addition, we present a polynomial-time algorithm for the related problem Exemplar Longest Common Subsequence in the special case that each mandatory symbol appears exactly once in one input sequence and at least once in the other input sequence. This answers an open question of Bonizzoni et al. We also show that Zero Exemplar Distance for multichromosomal genomes without gene order is fixed-parameter tractable in the general case if the parameter is the maximum number of chromosomes in each genome.     

Membrane connectivity estimated by digital image analysis of HER2 immunohistochemistry is concordant with visual scoring and fluorescence in situ hybridization results: algorithm evaluation on breast cancer tissue microarrays

Because metaplastic carcinoma of the breast encompasses a great variety of histopathology, diagnostic challenges abound, especially within the realm of cytology. The authors compiled and studied an eight-case series comprised of metaplastic breast carcinomas and lesions initially suspicious cytologically for metaplastic carcinoma in order to assess the degree of cytologic-histologic correlation and to identify recurring problematic themes surrounding the cytology-based diagnosis of this neoplasm. The cytologic and histologic slides from eight cases suspicious for metaplastic breast carcinoma diagnosed by fine needle aspiration (FNA) were collected and analyzed through a seven-year retrospective search of case files at our institution. Based on cytologic characteristics, the cases were separated into three groups. Group 1 consisted of three cases presenting with poorly differentiated adenocarcinoma and squamoid components on FNA. Group 2 was composed of two cases that featured a monophasic, malignant ductal cell population on cytology, while the cytologic specimens for the third group of cases presented with a mesenchymal component with or without a malignant glandular constituent. Cytologic-histologic correlation was present in two of three cases demonstrating a mesenchymal component, and there was 100% sensitivity in the cytologic detection of those mesenchymal elements. However, in only one of three cases was there an accurate cytologic diagnosis of metaplastic carcinoma when squamoid changes were present on FNA. Both cases demonstrating only malignant glandular elements on cytologic specimens revealed an additional component of malignant squamous differentiation upon the examination of mastectomy-derived tissue. These results indicate that squamous-like changes identified on FNA should be interpreted with caution and that sampling error remains a problematic recurrence in cytology. Regardless, there appears to be promise concerning the accurate cytologic diagnosis of metaplastic carcinoma when the lesion is characterized by a mesenchymal component. A study implementing a larger case number is essential in determining the significance of these findings.     

Inflammatory pseudotumor of the liver. Report of the fine needle aspiration cytologic findings in a case initially misdiagnosed as malignant

The fine needle aspiration (FNA) cytologic features are described in a case of inflammatory pseudotumor of the liver (xanthogranuloma), a disease generally regarded as of unknown etiology. The initial FNA findings were those of an acute exudative process, with atypical biliary duct epithelium and hepatocytes. These were interpreted as verifying the radiologic impression of a malignancy. Histologic study of subsequently resected nodules revealed the true nature of the case. As the lesion evolved, granulomatous inflammation supervened, characterized by numerous foamy histiocytes and lesser populations of plasma cells and lymphocytes. Numerous gram-positive cocci were readily demonstrated, suggesting that the lesion was an unusual tissue response to an intrahepatic bacterial infection. The lesion eventually resolved with prolonged antibiotic therapy.     

Regulation of Transaminase C Synthesis in Escherichia coli: Conditional Leucine Auxotrophy

The regulation of synthesis of the valine-alanine-alpha-aminobutyrate transaminase (transaminase C) was studied in Escherichia coli mutants lacking the branched-chain amino acid transaminase (transaminase B). An investigation was made of two strains, CU2 and CU2002, each carrying the same transaminase B lesion but exhibiting different growth responses on a medium supplemented with branched-chain amino acids. Both had the absolute isoleucine requirement characteristic of ilvE auxotrophs, but growth of strain CU2 was stimulated by valine, whereas that of strain CU2002 was markedly inhibited by valine. Strain CU2002 behaved like a conditional leucine auxotroph in that the inhibition by valine was reversed by leucine. Results of enzymatic studies showed that synthesis of transaminase C was repressed by valine in strain CU2002 but not in strain CU2. Inhibition by valine in strain CU2002 appears to be the combined effect of repression on transaminase C synthesis and valine-dependent feedback inhibition of alpha-acetohydroxy acid synthase activity, causing alpha-ketoisovalerate (and hence leucine) limitation. The ilvE markers of strains CU2 and CU2002 were each transferred by transduction to a wild-type genetical background. All ilvE recombinants from both crosses resembled strain CU2002 and were inhibited by valine in the presence of isoleucine. Thus, strain CU2 carries an additional lesion that allows it to grow on a medium containing isoleucine plus valine. It is concluded that conditional leucine auxotrophy is characteristic of mutants carrying an ilvE lesion alone.     

Fine needle aspiration cytology of chondroid syringoma. Report of a case

A case of chondroid syringoma of skin was diagnosed by fine needle aspiration cytology and confirmed by histopathologic study. The most important feature in both smears and cell blocks prepared from the aspirate was the presence of two distinct components: an epithelial component and a contrasting stromal component with a chondroid appearance. The clinical and pathologic features of chondroid syringoma are reviewed and the differential diagnosis is discussed, especially for the benign and malignant variants of this lesion.     

Pulmonary sclerosing hemangioma. Report of a case with diagnosis by fine needle aspiration.

Sclerosing hemangioma is a rare but well-recognized benign lesion of the lung. We report a case of pulmonary sclerosing hemangioma correctly diagnosed by fine needle aspiration (FNA) cytology. The sharp and smooth contour of the discrete mass in the left lower zone of the chest roentgenogram raised the possibility of a benign lesion, including pulmonary sclerosing hemangioma. The characteristic "blood spaces" with surrounding regular, bland polygonal tumor cells in the FNA smears provided an essential clue to the diagnosis of sclerosing hemangioma. It was confirmed by Surecut biopsy of the lesion. The patient remained well one year after the investigation and was spared an unnecessary diagnostic thoracotomy. The cytologic features and differential diagnoses of pulmonary sclerosing hemangioma are discussed. Besides delineating the cytologic characteristics of pulmonary sclerosing hemangioma, this case illustrates the importance of a careful clinicopathologic correlation, which should be exercised by the cytopathologist in all instances.