Interaction between the light quality and flowering time pathways in Arabidopsis

Flowering in Arabidopsis is accelerated by a reduced ratio of red light to far-red light (R/FR), which indicates the proximity of competitive vegetation. By exploiting the natural genetic variation in flowering time responses to low R/FR, we obtained further insight into the complex pathways that fine-tune the transition to flowering in Arabidopsis. The Bla-6 ecotype does not flower significantly earlier in response to low R/FR, but is still able to display other features of shade avoidance, suggesting branching of low R/FR signalling. Here we show that the muted flowering response of Bla-6 is due to high levels of the floral repressor FLOWERING LOCUS C (FLC), conferred by a combination of functional FLC and FRIGIDA ( FRI ) alleles with a 'weak' FY allele. The Bla-6 FY allele encodes a protein with a corrupted WW binding domain, and we provide evidence that this locus plays a key role in the natural variation in light quality-induced flowering in Arabidopsis. In Bla-6, FLC blocks promotion to flowering by reduced R/FR by inhibiting expression of the floral integrator FLOWERING LOCUS T ( FT ) in a dose-dependent manner. Reduction of FLC removes this obstruction, and Bla6 plants then exhibit strong induction of FT and flower early in response to a low R/FR signal. This paper illustrates the intricate interaction of environmental signals and genetic factors to regulate flowering in Arabidopsis.     

Lack of Adaptation of Chimeric GB Virus B/Hepatitis C Virus in the Marmoset Model: Possible Effects of Bottleneck

Approximately 3% of the world population is chronically infected with hepatitis C virus (HCV). GB virus B (GBV-B), a surrogate model for HCV, causes hepatitis in tamarins and is the virus phylogenetically most closely related to HCV. Previously we described a chimeric GBV-B containing an HCV insert from the 5′ noncoding region (NCR) that was adapted for efficient replication in tamarins (Saguinus species). We have also demonstrated that wild-type (WT) GBV-B rapidly adapts for efficient replication in a closely related species, the common marmoset (Callithrix jacchus). Here, we demonstrate that the chimeric virus failed to adapt during serial passage in marmosets. The chimeric virus was passaged four times through 24 marmosets. During passage, two marmoset phenotypes were observed: susceptible and partially resistant. Although appearing to adapt in a resistant animal during a prolonged and gradual increase in viremia, the chimeric GBV-B failed to replicate efficiently upon passage to a naïve marmoset. The resistance was specific to the chimeric virus, as the chimeric virus-resistant animals were susceptible to marmoset-adapted WT virus during rechallenge studies. Three isolates of the chimeric virus were sequenced, and 20 nucleotide changes were observed, including eight amino acid changes. Three unique changes were observed in the 5′ NCR chimeric insert, an area that is highly conserved in HCV. We speculate that the failure of the chimeric virus to adapt in marmosets might be due to a bottleneck that occurs at the time of infection of resistant animals, which may lead to a loss of fitness upon serial passage.Worldwide, approximately 170 million people are chronically infected with hepatitis C virus (HCV). The current approved therapy involves the combination of pegylated alpha interferon and ribavirin and has response rates for sustained viral clearance of 42% and 82% for genotypes 1 and 2/3, respectively (15, 29). However, a significant proportion of the population still develops serious disease as a consequence of HCV infection. HCV infection is the leading cause for liver transplantation in the United States (1, 50), and liver cancer due to HCV infection is one of the most rapidly increasing types of cancer in the United States (20).GB virus B (GBV-B) is a hepatotropic virus that causes hepatitis in tamarins and is the virus phylogenetically most closely related to HCV (33, 36, 44), and as such, GBV-B represents an important small-primate surrogate model for HCV infections. The history of the GB agent is complex and originates with the inoculation of tamarins with serum obtained from a surgeon with hepatitis (for a review, see reference 3); however there is little doubt that GBV-B is a tamarin virus, despite the fact that it has never been isolated from tamarins a second time. GBV-B has a very narrow host range for tamarins, marmosets, and other closely related New World monkeys (6, 23, 54). The GBV-B model overcomes a number of limitations encountered when working with HCV (3, 22). Due to the limited availability of tamarins, our lab and others (5, 16, 21, 23) initiated GBV-B studies in common marmosets (Callithrix jacchus), a small New World primate closely related to the tamarin (Saguinus sp.). The marmoset and tamarin represent less expensive, more readily available, and smaller animal models than the chimpanzee. While replication in marmosets is typically higher than what is observed in HCV-infected chimpanzees, reproducible infection profiles require some adaptation to this host (5, 54). Although robust replication of HCV in vitro is now possible using specific adapted strains of HCV (derivatives of the JFH1 and H77-S) and the Huh-7.5 cell line (4, 27, 52, 55, 56), the GBV-B primary hepatocyte culture system (2) may be more suitable for some studies, especially those involving specific aspects of the innate immune response and other viral host interactions.The organization of the GBV-B genome is very similar to that of HCV and the GBV-B polyprotein gene encodes 10 proteins analogous to the HCV proteins. The polyprotein of GBV-B has approximately 25 to 30% homology to that of HCV at the amino acid level (33), while the 5′ and 3′ noncoding regions (NCRs) are more divergent (7, 33, 40). The HCV and GBV-B 5′ NCRs are essential for both replication and translation. The structures are similar; however, GBV-B domain I is predicted to fold into two stem-loops (SL), compared to one SL in HCV, and the GBV-B 5′ NCR is longer due mainly to additional SL IIB and IIC that are not present in HCV (Fig. ​(Fig.1A)1A) (40). The 5′ NCR contains the internal ribosomal entry site (IRES), which can directly bind the 40S ribosomal subunit in order to initiate translation of the viral RNA (19, 38). cis RNA elements involved in RNA replication are also located in the HCV 5′ NCR (for a review, see reference 49). In GBV-B, 5′ NCR segments essential for genome replication have recently been identified (53).Open in a separate windowFIG. 1.(A) Predicted structures of the GBV-B (left) and HCV (right) 5′ NCRs. The scissors on GBV-B represent the sequence that was excised and replaced by the HCV insert, which is represented by scissors on the HCV 5′ NCR. The locations of mutations detected during sequencing are boxed: the first box identifies the deletion (ΔC) in a run of cytosines, and the second box identifies the polymorphisms present at two adjacent uracils (C, C/U). (Adapted from reference 40.) (B) Schematic of the GBV-B genome. During passage of GB/III^HC in tamarins, nine mutations were identified in virus from the T2 serum used to inoculate M1, and these nine mutations remained fixed in all marmoset isolates sequenced. Amino acid changes are indicated by dark arrows, silent mutations are indicated by asterisks, and NCR changes are indicated by dotted arrows.The utility of the GBV-B model was increased by the development of infectious cDNA clones that induced hepatitis upon intrahepatic inoculation of tamarins with in vitro-transcribed RNA (7, 31, 45). In order to further increase the use of GBV-B as a model for HCV, chimeras between GBV-B and HCV were constructed (16, 43, 48). In one chimera, a portion of the GBV-B 5′ NCR containing domain III, which is within the IRES functional domain, was replaced by an analogous region of HCV (40-43). The chimeric GB/III^HC retained IRES translational function and supported replication in tamarins (43). In this study, we examined the host range of this chimeric virus during serial passage in marmosets. We found that chimeric GBV-B failed to adapt during passage in marmosets. Marmosets infected with GB/III^HC displayed variable phenotypes ranging from susceptible to resistant, which appear to be due to a polymorphism in the marmoset population that also affects wild-type (WT) GBV-B (54). The failure of chimeric virus to adapt to replication in marmosets with the resistant phenotype was specific to the chimeric virus, and not the WT, and may involve several factors, including reduced replication capacity and the requirement to acquire multiple adaptive mutations. These barriers cumulatively may result in GB/III^HC experiencing a bottleneck in the resistant marmoset host.     

Protocol for the saMS trial (supportive adjustment for multiple sclerosis): a randomized controlled trial comparing cognitive behavioral therapy to supportive listening for adjustment to multiple sclerosis

Background

Multiple Sclerosis (MS) is an incurable, chronic, potentially progressive and unpredictable disease of the central nervous system. The disease produces a range of unpleasant and debilitating symptoms, which can have a profound impact including disrupting activities of daily living, employment, income, relationships, social and leisure activities, and life goals. Adjusting to the illness is therefore particularly challenging. This trial tests the effectiveness of a Cognitive Behavioural intervention compared to Supportive Listening to assist adjustment in the early stages of MS.

Methods/Design

This is a two arm randomized multi-centre parallel group controlled trial. 122 consenting participants who meet eligibility criteria will be randomly allocated to receive either Cognitive Behavioral Therapy or Supportive Listening. Eight one hour sessions of therapy (delivered over a period of 10 weeks) will be delivered by general nurses trained in both treatments. Self-report questionnaire data will be collected at baseline (0 weeks), mid-therapy (week 5 of therapy), post-therapy (15 weeks) and at six months (26 weeks) and twelve months (52 weeks) follow-up. Primary outcomes are distress and MS-related social and role impairment at twelve month follow-up. Analysis will also consider predictors and mechanisms of change during therapy. In-depth interviews to examine participants' experiences of the interventions will be conducted with a purposively sampled sub-set of the trial participants. An economic analysis will also take place.

Discussion

This trial is distinctive in its aims in that it aids adjustment to MS in a broad sense. It is not a treatment specifically for depression. Use of nurses as therapists makes the interventions potentially viable in terms of being rolled out in the NHS. The trial benefits from incorporating patient input in the development and evaluation stages. The trial will provide important information about the efficacy, cost-effectiveness and acceptability of the interventions as well as mechanisms of psychosocial adjustment.

Trial registration

Current Controlled Trials ISRCTN91377356     

The complex nature of humanD-locus determinants: Heterogeneity within Dw3

The HLA-A and B homozygous cell, ABR, was found to be mutually nonstimulatory with Dw3-homozygous test cell 16001 (EB), and so was considered to be Dw3-homozygous. However, family studies revealed a difference in theD-locus determinant(s) inherited from the father and mother. The cells carrying the determinants derived from the paternal1,8 haplotype (a _f ) consistently stimulated the lymphocytes bearing the determinants from the maternal1,8 haplotype (ainm), but thea _m haplotype products could not stimulate those of haplotypea _f . Sincea _m is included ina _f , cell ABR behaves in population studies as a Dw3-homozygous cell. Typing forD-locus determinants showed the father to be Dw3-positive, the mother Dw3-negative. The Dw3 determinant seems not homogeneous and this should be taken into account in explaining the results withD-locus homozygous typing cells.     

Ecology,conservation status,and phylogenetic placement of endemic Pristimantis frogs (Anura: Craugastoridae) in Trinidad and Tobago and genetic affinities to northern Venezuela

Trinidad and Tobago are home to three endemic species in the anuran genus Pristimantis, of which two (Pristimantis charlottevillensis and Pristimantis turpinorum) occur in Tobago alone and the third (Pristimantis urichi) is present on both islands. Earlier, the IUCN assessed the conservation status of these species as: P. urichi, Endangered (EN); P. charlottevillensis, Least Concern (LC); P. turpinorum, Vulnerable (VU). However, these assessments were based on very little field-based evidence. Here, we present survey results which contributed to reassessments as LC, VU and Data Deficient for these three species, respectively. Despite the close proximity of Trinidad to northern Venezuela, the islands do not share any Pristimantis species with the mainland, which holds a rich endemicity of Pristimantis regionally. In this study, we used genetic sequencing from several island populations and compared them to northern Venezuelan endemics to assess genetic divergence for the first time. The time tree analyses found that only the northern Tobago species P. turpinorum is closely related to mainland Pristimantis, with a genetic split dating to the Late Miocene, suggesting a vicariant event of mainland and island species. Pristimantis urichi, although identical between the two islands, remains highly divergent from the mainland species. Similar results were found for P. charlottevillensis. In addition, there was a high level of divergence between P. urichi and P. charlottevillensis. These findings indicate different island colonization events by different lineages. Sequencing other Venezuelan species remains pivotal to unravel the complexity of the colonization episodes in the region, likely influenced by the changing topography and multiple connection and isolation episodes of the islands by eustatic sea-level changes.     

Setting up a pragmatic clinical trial in a low-resource setting: A qualitative assessment of GoLBeT,a trial of podoconiosis management in Northern Ethiopia

BackgroundClinical trials are often perceived as being expensive, difficult and beyond the capacity of healthcare workers in low-resource settings. However, in order to improve healthcare coverage, the World Health Organization (WHO) World Health Report 2013 stated that all countries need to become generators as well as recipients of data. This study is a methodological examination of the steps and processes involved in setting up the Gojjam Lymphoedema Best Practice Trial (GoLBeT; ISRCTN67805210), a highly pragmatic clinical trial conducted in northern Ethiopia. Challenges to the trial and strategies used to deal with them were explored, together with the reasons for delays.Methodology and principal findingsQualitative research methods were used to analyse emails and reports from the period between trial inception and recruitment. This analysis was complemented by interviews with key informants from the trial operational team. The Global Health Research Process Map was used as a framework against which to compare the steps involved in setting up the trial. A mini-group discussion was conducted with the trial operational team after study completion for reflection and further recommendations.This study showed that the key areas of difficulty in setting up and planning this trial were: the study design, that is, deciding on the study endpoint, where and how best to measure it, and assuring statistical power; recruitment and appropriate training of staff; planning for data quality; and gaining regulatory approvals. Collaboration, for example with statisticians, the trial steering committee, the study monitors, and members of the local community was essential to successfully setting up the trial.Conclusions and significanceLessons learnt from this trial might guide others planning pragmatic trials in settings where research is not common, allowing them to anticipate possible challenges and address them through trial design, planning and operational delivery. We also hope that this example might encourage similar pragmatic studies to be undertaken. Such studies are rarely undertaken or locally led, but are an accessible and efficient way to drive improved outcomes in public health.