The complex polyploid genome architecture of sugarcane

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds

Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.

Spirodela, or duckweed, is a basal monocotyledonous plant with both pharmaceutical and commercial value. Here, the authors sequence the genome of Spirodela polyrhiza, suggesting its genome has evolved by neotenous reduction and clonal propagation, and provide a platform for future comparative genomic studies in angiosperms.

The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks

Animal pigment patterns are important for a range of functions, including camouflage and communication. Repeating pigment patterns, such as stripes, bars and spots have been of particular interest to developmental and theoretical biologists, but the genetic basis of natural variation in such patterns is largely unexplored. In this study, we identify a difference in a periodic pigment pattern among juvenile threespine sticklebacks (Gasterosteus aculeatus) from different environments. Freshwater sticklebacks exhibit prominent vertical bars that visually break up the body shape, but sticklebacks from marine populations do not. We hypothesize that these distinct pigment patterns are tuned to provide crypsis in different habitats. This phenotypic difference is widespread and appears in most of the freshwater populations that we sampled. We used quantitative trait locus (QTL) mapping in freshwater-marine F2 hybrids to elucidate the genetic architecture underlying divergence in this pigmentation pattern. We identified two QTL that were significantly associated with variation in barring. Interestingly, these QTL were associated with two distinct aspects of the pigment pattern: melanophore number and overall pigment level. We compared the QTL locations with positions of known pigment candidate genes in the stickleback genome. We also identified two major QTL for juvenile body size, providing new insights into the genetic basis of juvenile growth rates in natural populations. In summary, although there is a growing literature describing simple genetic bases for adaptive coloration differences, this study emphasizes that pigment patterns can also possess a more complex genetic architecture.

A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies

A genetic linkage map for the ectomycorrhizal basidiomycete Laccaria bicolor was constructed from 45 sib-homokaryotic haploid mycelial lines derived from the parental S238N strain progeny. For map construction, 294 simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers were employed to identify and assay loci that segregated in backcross configuration. Using SNP, RAPD and SSR sequences, the L. bicolor whole-genome sequence (WGS) assemblies were aligned onto the linkage groups. A total of 37.36 Mbp of the assembled sequences was aligned to 13 linkage groups. Most mapped genetic markers used in alignment were colinear with the sequence assemblies, indicating that both the genetic map and sequence assemblies achieved high fidelity. The resulting matrix of recombination rates between all pairs of loci was used to construct an integrated linkage map using JoinMap. The final map consisted of 13 linkage groups spanning 812 centiMorgans (cM) at an average distance of 2.76 cM between markers (range 1.9-17 cM). The WGS and the present linkage map represent an initial step towards the identification and cloning of quantitative trait loci associated with development and functioning of the ectomycorrhizal symbiosis.

Hyperbaric oxygen therapy (HBO) for the treatment of an epidural abscess in the posterior fossa in an 8-month-old infant

Epidural abscesses in children are extremely rare, especially in the posterior fossa. In some cases antibiotic therapy and surgical drainage are insufficient for complete healing. We present the case of an 8-month-old boy who developed an epidural abscess in the posterior fossa after repeated surgical procedures for retrocerebellar arachnoid cysts and hydrocephalus. We decided to use adjuvant hyperbaric oxygen therapy (HBO) to avoid removal of the bone and the existing ventriculoperitoneal shunt. In this way osteomyelitis, potentially leading to bone removal and shunt infection, could be prevented. HBO is a relatively safe, noninvasive and cost-effective therapy to improve healing of chronic and deep-seated wound infections. To our knowledge HBO has never been used before in such a young child in neurosurgery. Multidisciplinary management is recommended to optimize treatment.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

The impact of past alcohol use on treatment response rates in patients with chronic hepatitis C

BACKGROUND

Studies have shown that past alcohol consumption reduces response rates in patients with chronic hepatitis C treated with interferon monotherapy.

AIM

To clarify the importance of alcohol consumption on response rates in patients undergoing treatment with pegylated interferon and ribavirin.

METHODS

In a single centre, prospective study, median daily alcohol consumption (determined by previously validated method) and quartiles of alcohol consumption were calculated. Univariate and binary logistic regression analyses were performed using treatment response status as the dependent variable.

RESULTS

Overall, in an intention-to-treat analysis, 34 of 115 patients (30%) responded to treatment. In univariate analysis, black patients, especially those with hepatitis C virus genotype 1, high viral load and low alanine aminotransferase were significantly less likely to respond. Predictors of response by regression analysis included alcohol <30 g/day (OR=3.02, 95% CI: 1.02-8.93; P=0.04), non-genotype 1 status (OR=1.98, 95% CI: 1.03-3.80; P=0.04) and non-black race (OR=2.79, 95% CI: 1.33-5.85; P=0.006).

CONCLUSIONS

Median daily alcohol use >30 g/day is associated with failure to respond to pegylated interferon and ribavirin for treatment of hepatitis C. Past alcohol use should be evaluated when considering treatment for hepatitis C.

Comparative DNA sequence analysis of mouse and human protocadherin gene clusters

The genomic organization of the human protocadherin alpha, beta, and gamma gene clusters (designated Pcdh alpha [gene symbol PCDHA], Pcdh beta [PCDHB], and Pcdh gamma [PCDHG]) is remarkably similar to that of immunoglobulin and T-cell receptor genes. The extracellular and transmembrane domains of each protocadherin protein are encoded by an unusually large "variable" region exon, while the intracellular domains are encoded by three small "constant" region exons located downstream from a tandem array of variable region exons. Here we report the results of a comparative DNA sequence analysis of the orthologous human (750 kb) and mouse (900 kb) protocadherin gene clusters. The organization of Pcdh alpha and Pcdh gamma gene clusters in the two species is virtually identical, whereas the mouse Pcdh beta gene cluster is larger and contains more genes than the human Pcdh beta gene cluster. We identified conserved DNA sequences upstream of the variable region exons, and found that these sequences are more conserved between orthologs than between paralogs. Within this region, there is a highly conserved DNA sequence motif located at about the same position upstream of the translation start codon of each variable region exon. In addition, the variable region of each gene cluster contains a rich array of CpG islands, whose location corresponds to the position of each variable region exon. These observations are consistent with the proposal that the expression of each variable region exon is regulated by a distinct promoter, which is highly conserved between orthologous variable region exons in mouse and human.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

A physical map of the human genome

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

[Activated protein C resistance and cardiolipin antibodies in leg ulcers]

BACKGROUND

We conducted a prospective study to determine the prevalence of activated protein C resistance and anticardiolipin antibodies in leg ulcers, whatever venous, arterial or arteriovenous.

PATIENTS AND METHODS

One hundred fifteen patients hospitalized for leg ulcers, without antiphospholipid syndrome were included. The vascular abnormalities were studied by clinical examination, Doppler, duplex Doppler and, when required, arteriography. Activated protein C resistance was isolated by a "classic" test (normalized APTT ratio in PCa presence or absence) and by a "second generation test" (by preliminary dilution with deficient factor V plasma). All patients with abnormal results on the second test were screened for the factor V Leiden (by PCR amplication with use of restriction enzymes). Anticardiolipin antibodies were investigated with an ELISA method with Harris standards as reference, in which the positive threshold was established at 20 units.

RESULTS

Among these 115 patients, 50 venous (43.5 p. 100), 23 arterial (20 p. 100), 42 arteriovenous (36.5 p. 100) leg ulcers were identified. Activated protein C resistance was isolated in 12 cases (10.4 p. 100) (heterozygous carriers): 7 venous ulcers, 3 arteriovenous, 2 arterial. Anticardiolipin antibodies were measured at significant level in 49 cases (42.6 p. 100): 21 venous ulcers, 18 arteriovenous, 10 arterial.

DISCUSSION

In this study, there was no statistical difference between the activated protein C resistance prevalence in leg ulcers when compared with Lorraine population (p=0.27). Factor V Leiden or anticardiolipin antibodies abnormalities were isolated in 56 cases (48.7 p. 100) without statistical difference between the 3 types of ulcers. Finally, the pathophysiology of venous, arterial and arteriovenous leg ulcers remains complex, suggesting several coagulation perturbations.

[Contact dermatitis due to ethyl alcohol: how to perform patch tests?]

INTRODUCTION

Ethyl alcohol sensitization is rare and can induce immediate contact urticaria or delayed eczema. Patch tests performed with ethanol can provoke an irritative reaction and are not well codified.

CASE-REPORTS

We report on 4 cases of contact dermatitis due to alcohol in 4 women. Eczema was due to alcohol contained in the reservoir of a transdermal transfer system with estrogens in 2 cases and related to the application of alcoholized antiseptic lotions in the other 2 cases. In 2/4 cases we observed a co-sensitization with corticosteroids.

METHODS

Patch tests were performed with alcohol at 95 degrees diluted at 70 p. 100 and at 10 p. 100 in water and read after 20 minutes then on day 2 and day 4.

RESULTS

Positive results were obtained in 4/4 cases when alcohol was tested diluted at 70 p. 100 in water and in 3/4 cases when diluted at 10 p. 100 in water. No irritant reaction was observed in 140 negative controls.

DISCUSSION

Immediate after 20 minutes and delayed readings of patch tests performed with ethyl alcohol diluted at 70 p. 100 seem to be convenient in diagnosing cutaneous delayed hypersensitivity to alcohol. Co-sensitization between corticosteroids and alcohol could be due to an aldehyde deshydrogenase deficiency.

[Intestinal parasitosis in irritable colon]

Parasitic infestation of the intestinal tract was investigated in a prospective study of 177 patients from southern Europe and Turkey. In a group of patients (n = 127) who attended the Medical Outpatients Department because of abdominal pain, pathogenic parasites were isolated from a single stool sample in 69 (54%). 19 patients had 2 or more parasites. 22 out of 25 patients reviewed after treatment were free of parasites, and 17 were symptom-free. Abdominal pain persisted unchanged in 8 patients. In a second group of patients (n = 50) with extraabdominal symptoms, 11 (22%) had pathogenic parasites in stool. Multiple infestation did not occur in this group. The results show that in this population group stool examination for parasites should be carried out routinely in the investigation of abdominal pain. The high prevalence rate possibly justifies a search for parasites even where there are no intestinal symptoms.

[The differential diagnosis of indolent ulcers upon return from the Tropics: frambesia]

A 26-year-old patient was referred for investigation of chronic skin ulcerations which had appeared 2 months after a one-week stay in the Ivory Coast. The diagnosis was established clinically and serologically and the patient was successfully treated with penicillin. Even if yaws is a rare imported disease in Switzerland, it should always be considered in differential diagnosis of painless skin ulcerations in travellers returning from tropical countries, bearing in mind that the number of cases of yaws has increased in several tropical countries.

Clinicopathologic effects of cancer chemotherapeutic agents on human buccal mucosa

Specimens of buccal mucosa obtained at autopsy from 216 patients were examined for histopathologic alterations. Atrophic oral epithelium was found in thirty cases. A retrospective study of the hospital records revealed that thirteen of these latter patients had been on a cancer chemotherapeutic regimen prior to death. There was a significantly higher incidence of atrophy in the chemotherapy group (p less than 0.001) than in control patients. These findings, as well as the expected inherent susceptibility of rapidly replicating oral epithelial cells to metabolic inhibitors, suggest a causal relationship between oral atrophy and the administration of cancer chemotherapeutic agents. This atrophy may therefore represent a preliminary stage of mucosal alteration that ultimately progresses to the clinical sequelae of stomatitis and oral ulcerations frequently encountered during cancer chemotherapy. Some alternative mechanisms are also discussed.