A homozygous loss-of-function mutation in inositol monophosphatase 1 (IMPA1) causes severe intellectual disability.

The genetic basis of intellectual disability (ID) is extremely heterogeneous and relatively little is known about the role of autosomal recessive traits. In a field study performed in a highly inbred area of Northeastern Brazil, we identified and investigated a large consanguineous family with nine adult members affected by severe ID associated with disruptive behavior. The Genome-Wide Human SNP Array 6.0 microarray was used to determine regions of homozygosity by descent from three affected and one normal family member. Whole-exome sequencing (WES) was performed in one affected patient using the Nextera Rapid-Capture Exome kit and Illumina HiSeq2500 system to identify the causative mutation. Potentially deleterious variants detected in regions of homozygosity by descent and not present in either 59 723 unrelated individuals from the Exome Aggregation Consortium (Browser) or 1484 Brazilians were subject to further scrutiny and segregation analysis by Sanger sequencing. Homozygosity-by-descent analysis disclosed a 20.7-Mb candidate region at 8q12.3-q21.2 (lod score: 3.11). WES identified a homozygous deleterious variant in inositol monophosphatase 1 (IMPA1) (NM_005536), consisting of a 5-bp duplication (c.489_493dupGGGCT; chr8: 82,583,247; GRCh37/hg19) leading to a frameshift and a premature stop codon (p.Ser165Trpfs*10) that cosegregated with the disease in 26 genotyped family members. The IMPA1 gene product is responsible for the final step of biotransformation of inositol triphosphate and diacylglycerol, two second messengers. Despite its many physiological functions, no clinical phenotype has been assigned to this gene dysfunction to date. Additionally, IMPA1 is the main target of lithium, a drug that is at the forefront of treatment for bipolar disorder.

Whole-Genome Sequence of a Bordetella pertussis Brazilian Vaccine Strain.

Despite the reduction in incidence after vaccination, pertussis disease is still considered a public health problem worldwide, mainly due to recent and potential new outbreaks. We report here the complete genome of the Bordetella pertussis Butantan strain used in the Brazilian National Immunization Program as a whole-cell pertussis antigen to compose vaccines such as DTwP (diphtheria, tetanus, and whole-cell pertussis).

Exome sequencing for mucolipidosis III: Detection of a novel GNPTAB gene mutation in a patient with a very mild phenotype.

Mucolipidosis II and III alpha/beta (ML II/III alpha/beta) are rare autosomal recessive lysosomal storage diseases that are caused by a deficiency of UDP-GlcNAc:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase, the enzyme responsible for the synthesis of the mannose 6-phosphate targeting signal on lysosomal hydrolases. A Brazilian patient suspected of having a very mild ML III was investigated using whole next-generation sequencing (NGS). Two mutations in the GNPTAB gene were detected and confirmed to be in trans status by parental analysis: c.1208T>C (p.Ile403Thr), previously reported as being pathogenic, and the novel mutation c.1723G>A (p.Gly575Arg). This study demonstrates the effectiveness of using whole NGS for the molecular diagnosis of very mild ML III alpha/beta patients.

Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis.

Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in accidental hosts, including humans. Complete genome sequencing of Leptospira interrogans serovar Copenhageni and comparative analysis with the available Leptospira interrogans serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. A broad array of transcriptional regulation proteins and two new families of afimbrial adhesins which contribute to host tissue colonization in the early steps of infection were identified. Differences in genes involved in the biosynthesis of lipopolysaccharide O side chains between the Copenhageni and Lai serovars were identified, offering an important starting point for the elucidation of the organism's complex polysaccharide surface antigens. Differences in adhesins and in lipopolysaccharide might be associated with the adaptation of serovars Copenhageni and Lai to different animal hosts. Hundreds of genes encoding surface-exposed lipoproteins and transmembrane outer membrane proteins were identified as candidates for development of vaccines for the prevention of leptospirosis.

Comparative genomic analysis of plant-associated bacteria.

This review deals with a comparative analysis of seven genome sequences from plant-associated bacteria. These are the genomes of Agrobacterium tumefaciens, Mesorhizobium loti, Sinorhizobium meliloti, Xanthomonas campestris pv campestris, Xanthomonas axonopodis pv citri, Xylella fastidiosa, and Ralstonia solanacearum. Genome structure and the metabolism pathways available highlight the compromise between the genome size and lifestyle. Despite the recognized importance of the type III secretion system in controlling host compatibility, its presence is not universal in all necrogenic pathogens. Hemolysins, hemagglutinins, and some adhesins, previously reported only for mammalian pathogens, are present in most organisms discussed. Different numbers and combinations of cell wall degrading enzymes and genes to overcome the oxidative burst generally induced by the plant host are characterized in these genomes. A total of 19 genes not involved in housekeeping functions were found common to all these bacteria.

The genome of the natural genetic engineer Agrobacterium tumefaciens C58.

The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.

Glucides of Cnidium monnieri fruit.

From the fruit of Cnidium monnieri Cusson (Umbelliferae), two glucides were isolated together with other known glucides. Their structures were clarified as glycerol 2-O-alpha-L-fucopyranoside and D-quinovitol (6-deoxy-D-glucitol), respectively.

Water-soluble constituents of ajowan.

From the water-soluble portion of the methanol extract of the fruit of Carum ajowan (ajowan), which has been used as a spice and medicine, 25 compounds, including five new monoterpenoid glucosides, a new monoterpenoid, two new aromatic compound glucosides, and two new glucides, were obtained. Their structures were clarified by spectral investigation.

Water-soluble constituents of Glehnia littoralis fruit.

From the water-soluble portion of the methanol extract of the fruit of Glehnia littoralis Fr. SCHMIDT ex MIQ. (Umbelliferae; "hamabofu" in Japanese), thirty compounds, including three new monoterpenoids and a new monoterpenoid glucoside, a new benzofuran glucoside, a new alkyl glucoside, and a new glucide, were obtained. Their structures were clarified by spectral investigation.

The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis.

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.

Flavonol glycosides from Asplenium foreziense and its five related taxa and A. incisum.

The flavonoids of Asplenium foreziense, A. fontanum subsp. fontanum and subsp. pseudofontanum, A. obovatum subsp. obovatum var. obovatum and var. protobillotii, A. obovatum subsp. lanceolatum, and A. incisum were isolated and identified for chemotaxonomic survey. A major constituent of all taxa was kaempferol 3-O-gentiobioside. As minor compounds, kaempferol 3,7-O-glycoside and/or kaempferol 3-O-glycoside were found in A. fontanum, A. obovatum and A. foreziense, and kaempferol 3-O-gentiobioside-4'-O-glucoside, kaempferol 3-O-glucoside and quercetin 3-O-diglucoside in A. incisum. It was suggested that A. foreziense, A. fontanum including subsp. pseudofontanum and A. obovatum including subsp. lanceolatum are not only morphologically but also chemotaxonomically related. The East Asian A. incisum was chemically and geographically different from these taxa.

Three new sesquiterpenoid glucosides of Ficus pumila fruit.

As the glycosyl constituents of Ficus pumila L. fruits (Moraceae), three new sesquiterpenoid glucosides, pumilasides A, B and C were isolated together with benzyl beta-D-glucopyranoside, (E)-2-methyl-2-butenyl beta-D-glucopyranoside and rutin. Their structures were characterized as (1S,4S,5R,6R,7S,10S)-1,4,6-trihydroxyeudesmane 6-O-beta-D-glucopyranoside, (1S,4S,5S,6R,7R,10S)-1,4-dihydroxymaaliane 1-O-beta-D-glucopyranoside and 10 alpha, 11-dihydroxycadin-4-ene 11-O-beta-D-glucopyranoside by spectral and chemical methods.

Chalcone and flavonol glycosides from Asarum canadense (Aristolochiaceae).

Two chalcone glycosides were isolated, together with seven known flavonol glycosides, from the leaves of Asarum canadense. The structures of the chalcone glycosides were established as chalcononaringenin 2',4'-di-O-glucoside and chalcononaringenin 2'-O-glucoside-4'-O-gentiobioside by chemical, UV, FAB MS, 1H and 13C NMR evidence.

Primary anaplastic large-cell lymphoma of the skin. A case report suggesting that regressing atypical histiocytosis and lymphomatoid papulosis are subsets.

A patient with primary anaplastic large-cell lymphoma of the skin with characteristic clinical findings is described. The diagnosis was made on the basis of histologic and immunohistochemical findings. The phenotype of the tumor cells was not determined, but rearrangement of the T-cell receptor beta gene indicated that the tumor was of T-cell lineage. Despite high-grade malignancy of the tumor cells, the patient unexpectedly had a benign clinical course. The findings in this case suggest that regressing atypical histiocytosis and lymphomatoid papulosis type A are subsets of anaplastic large-cell lymphoma.

Acquired dermal melanocytosis of the hand: a new clinical type of dermal melanocytosis.

We report a 22-year-old man with acquired dermal melanocytosis on the hand which developed without any history of previous inflammation. He had no history of contact with or oral administration of any drugs or metals which might have caused pigmentation. Histopathologically, spindle-shaped dermal melanocytes were observed running parallel to the collagen bundles and scattered in all portions of the dermis. The dopa reaction of these cells was positive. Ultrastructurally, dermal melanocytes containing numerous melanosomes (stages II to IV) which were surrounded by the extracellular sheath were observed. Differential diagnosis of other dermal melanocytosis was discussed.

Squamous cell carcinoma developing in epidermolysis bullosa dystrophica.

Two patients with epidermolysis bullosa dystrophica recessiva who had squamous cell carcinoma are presented. Case 1 is a 40-year-old woman who had ulcers on her left lower leg. Case 2 is a 42-year-old man who had a tumor on his left first toe. Wide surgical excision with skin coverage by autograft was performed in case 1. Amputation of the toe in case 2 was performed. A review of the cases of epidermolysis bullosa dystrophica associated with cancer reported in Japan is also presented.

Crusted scabies in acquired selective IgA deficiency.

Crusted scabies, an unusual clinical variant of human scabies mite infestation, is usually reported in cases of gross debility, mental deficiency, or immunosuppression. We report here the occurrence of crusted scabies in a 40-year-old man with acquired selective IgA deficiency suspected to be caused by long-term medication with phenytoin for epilepsy.

Contraction phenomenon of type I collagen gel by melanoma cells.

In order to study the interaction between melanoma cells and collagen, B16 murine melanoma cells were embedded and cultured in type I collagen gel. Melanoma cells cultured in the collagen gel became elongated, as compared with those cultured on plastic, and some of them assumed a dendritic form. The gel contracted very slowly but steadily during culturing of melanoma cells, as in the experiment using fibroblasts. On the 20th day of culture the area of the gel accounted for only 32% of that when culture started. This contraction was enhanced by retinoic acid, which is known to induce cell differentiation. The contractility of the gel differed between various lines of melanoma cells. The present observations raise the possibility of interaction between melanoma cells and type I collagen.