Sequence and structural analysis of the rfb (O antigen) gene cluster from a group C1 Salmonella enterica strain.

The rfb (O antigen) gene cluster of a group C1 Salmonella enterica strain was sequenced; it comprised seven open reading frames which precisely replaced the 16 open reading frames of a group B strain. Two genes of the mannose biosynthetic pathway were present: rfbK (phosphomannomutase) had a G+C content of 0.61 and had only 40% identity to rfbK of group B but was very similar to cpsG of the capsular polysaccharide pathway with 96% identity, whereas rfbM [guanosine diphosphomannose (GDP-Man) pyrophosphorylase] had a G+C content of 0.39. Other genes had G+C contents ranging from 0.24 to 0.28. rfbM(C1) and rfbM(B) had 60% identity, which is much less than expected within a species, but nonetheless indicates a much more recent common ancestor than for rfbK. The other genes showed much lower or no similarity to rfb genes of other S. enterica strains. It appears that the gene cluster evolved outside of Salmonella in a species with low G+C content: the rfbM gene presumably derives from that period whereas the rfbK gene appears to have arisen after transfer of the cluster to S. enterica by duplication of the S. enterica cpsG gene, presumably replacing an rfbK gene of low G+C content.     

小麦幼苗中过氧化物歧化酶活性与幼苗脱水忍耐力相关性的研究

本文着重探讨当前国际上提出的一种植物抗旱机制的新理论——即生物自由基与植物保护酶系统间相互作用的理论。在水分逆境情况下,植物细胞内自由基产生和清除的平衡遭到破坏,过剩的自由基会伤害细胞膜系统。过氢化物歧化酶是氧自由基的清除剂,因此它的活性的高低应与植物的抗旱能力密切相关。以小麦幼苗为材料,采用光化学方法测定了过氧化物歧化酶活性,同时测定幼苗的脱水耐受力,发现在不同组织和器官中,在不同发育阶段的幼苗中,二者均存在有正相关性。此外,还测定了幼苗脱水前后过氧化物歧化酶活性的变化,发现酶活性在脱水处理时升高。我们推测小麦幼苗经受干旱的过程中,细胞内可能包含生物自由基的有害作用。     

Manufacturing development and clinical production of NKG2D chimeric antigen receptor–expressing T cells for autologous adoptive cell therapy

Background aims

Adoptive cell therapy employing natural killer group 2D (NKG2D) chimeric antigen receptor (CAR)-modified T cells has demonstrated preclinical efficacy in several model systems, including hematological and solid tumors. We present comprehensive data on manufacturing development and clinical production of autologous NKG2D CAR T cells for treatment of acute myeloid leukemia and multiple myeloma (ClinicalTrials.gov Identifier: NCT02203825). An NKG2D CAR was generated by fusing native full-length human NKG2D to the human CD3ζ cytoplasmic signaling domain. NKG2D naturally associates with native costimulatory molecule DAP10, effectively generating a second-generation CAR against multiple ligands upregulated during malignant transformation including MIC-A, MIC-B and the UL-16 binding proteins.

Extinct,obscure or imaginary: The lizard species with the smallest ranges

Aim

Small geographic ranges make species especially prone to extinction from anthropogenic disturbances or natural stochastic events. We assemble and analyse a comprehensive dataset of all the world's lizard species and identify the species with the smallest ranges—those known only from their type localities. We compare them to wide‐ranging species to infer whether specific geographic regions or biological traits predispose species to have small ranges.

Location

Global.

Methods

We extensively surveyed museum collections, the primary literature and our own field records to identify all the species of lizards with a maximum linear geographic extent of <10 km. We compared their biogeography, key biological traits and threat status to those of all other lizards.

Results

One in seven lizards (927 of the 6,568 currently recognized species) are known only from their type localities. These include 213 species known only from a single specimen. Compared to more wide‐ranging taxa, they mostly inhabit relatively inaccessible regions at lower, mostly tropical, latitudes. Surprisingly, we found that burrowing lifestyle is a relatively unimportant driver of small range size. Geckos are especially prone to having tiny ranges, and skinks dominate lists of such species not seen for over 50 years, as well as of species known only from their holotype. Two‐thirds of these species have no IUCN assessments, and at least 20 are extinct.

Main conclusions

Fourteen per cent of lizard diversity is restricted to a single location, often in inaccessible regions. These species are elusive, usually poorly known and little studied. Many face severe extinction risk, but current knowledge is inadequate to properly assess this for all of them. We recommend that such species become the focus of taxonomic, ecological and survey efforts.

     

High-throughput marker assays for <Emphasis Type="Italic">FaRPc2</Emphasis>-mediated resistance to Phytophthora crown rot in octoploid strawberry

Phytophthora crown rot (PhCR) caused by Phytophthora cactorum is a destructive disease of the allo-octoploid cultivated strawberry (Fragaria ×ananassa Duch). Many major strawberry cultivars grown worldwide are susceptible to PhCR. Resistance is conferred by the recently-discovered FaRPc2 locus, but high-throughput markers are not yet available for marker-assisted breeding. In the current study, we developed DNA markers for two haplotypes at the FaRPc2 locus associated with resistance, H2 and H3. Marker validation and marker-assisted selection were performed in University of Florida (UF) breeding population. Seven single nucleotide polymorphism-based high resolution melting (HRM) markers linked to H2 and four HRM markers for H3 were developed. One HRM marker, RPCHRM3 linked to H3, was converted to a Kompetitive Allele Specific PCR (KASP) marker. To further examine the utility of the markers, they were screened in University of California Davis cultivars with known phenotypes as well as in 20 diverse accessions with phenotypes that are reported in the literature and that are preserved at the USDA-ARS National Clonal Germplasm Repository, in Corvallis, Oregon. The most informative markers for FaRPc2 resistance are being implemented in the UF strawberry breeding program to improve PhCR resistance.     

Delineation of the frequency and boundary of chromosomal copy number variations in paediatric neuroblastoma

Neuroblastoma, the most common solid tumour in early childhood, is characterized by very frequent chromosomal copy number variations (CNVs). While chromosome 2p amplification, 17q gain, 1p and 11q deletion in human neuroblastoma tissues are well-known, the exact frequencies and boundaries of the chromosomal CNVs have not been delineated. We analysed the publicly available single nucleotide polymorphism (SNP) array data which were originally generated by the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative, defined the frequencies and boundaries of chromosomes 2p11.2 – 2p25.3 amplification, 17q11.1-17q25.3 gain, 1p13.3-1p36.33 deletion and 11q13.3-11q25 deletion in neuroblastoma tissues, and identified chromosome 7q14.1 (Chr7:38254795-38346971) and chromosome 14q11.2 (Chr14:21637401-22024617) deletion in blood and bone marrow samples from neuroblastoma patients, but not in tumour tissues. Kaplan Meier analysis showed that double deletion of Chr7q14.1 and Chr14q11.2 correlated with poor prognosis in MYCN gene amplified neuroblastoma patients. In conclusion, the oncogenes amplified or gained and tumour suppressor genes deleted within the boundaries of chromosomal CNVs in tumour tissues should be studied for their roles in tumourigenesis and as therapeutic targets. Focal deletions of Chr7q14.1 and Chr14q11.2 together in blood and bone marrow samples from neuroblastoma patients can be used as a marker for poorer prognosis and more aggressive therapies.     

Influence of landscape heterogeneity on the functional connectivity of Allegheny woodrats (<Emphasis Type="Italic">Neotoma magister</Emphasis>) in Virginia

Allegheny woodrats (Neotoma magister) exist as groups of metapopulations due to their dependence on naturally disjunct rocky outcrops in the eastern United States. Severe demographic declines of Allegheny woodrats have occurred in many parts of the range due to a myriad of interacting processes, therefore identifying factors that help maintain the integrity of metapopulations is needed to guide conservation efforts. One factor considered critical to metapopulation persistence is maintaining functional connectivity. Therefore, our objective was to identify landscape factors that influence gene flow in Allegheny woodrats. We sampled 159 individuals from throughout the distribution in Virginia, genotyped them at 22 microsatellite loci, and modeled effects of land cover, roads, large rivers, and elevation on gene flow. The model that parameterized areas?≤?750 m in elevation as a barrier to gene flow performed best among the tested models, which indicates that functional connectivity is highest in high elevation habitats. We found little evidence for anthropogenic factors influencing gene flow, but continued study across extant metapopulations is needed in more peripheral areas to evaluate if anthropogenic barriers impact functional connectivity. Overall, our study emphasizes the importance of considering elevation for maintaining functional connectivity of Allegheny woodrats in the face of ongoing demographic declines in the eastern United States.     

Pollen and charcoal studies at the Wolf Willow site,Wanuskewin Heritage Park,Saskatoon, Canada

This study aims to determine whether pollen and charcoal analyses of terrestrial samples from the Wolf Willow archaeological site at Wanuskewin Heritage Park, Saskatoon, Saskatchewan, Canada could help provide the sorts of data necessary to evaluate the role that environmental conditions may have played in the 6,000 year occupational history of the park. The results indicate that pollen and charcoal were sufficiently preserved for analysis and that pollen assemblages were not significantly affected by downwash or differential preservation. Environmental reconstructions show relatively moist conditions at ca. 4,850 bp continuing into the Oxbow period (ca. 4,800–4,100 bp), when a drying trend developed. The McKean period (ca. 4,200–3,000 bp) reflects a broadly dry period with increasing moisture through time. A hiatus interrupts the record, above which Prairie Side-Notched data (ca. 1,100–600 bp) reveal relatively moist conditions, followed by decreased moisture during Plains Side-Notched times (ca. 600–200 bp), which continued into the recent/historic period. Analyses also indicated possible distinctions between roasting and stone boiling features, repeated spring-time occupation, and task-dependant firewood selection. Comparison of the Wolf Willow records to palaeoenvironmental reconstructions derived from lake cores and other proxy data placed these results within the broader literature on several millennia of Northern Plains climatic and environmental variation. Thus, these results clearly indicate the high potential of such research to address questions regarding human-environment interaction and the role that palaeoenvironmental conditions may have played in drawing indigenous peoples from across the Northern Plains to repeatedly gather at Wanuskewin Heritage Park.     

Identifying behavioral states and habitat use of acoustically tracked humpback whales in Hawaii

Although humpback whales have been well‐studied on their Hawaiian breeding grounds, it is difficult to track individual animals over long distances without tags, particularly when they move offshore. Here, singing humpback whales were localized in three dimensions on the Pacific Missile Range Facility off Kauai, Hawaii, located between 20 km and 80 km offshore, from January 2011 through June 2014. Detailed behavioral analyses were conducted on the resulting tracks. One hundred and eight individual tracks were identified and metrics of these tracks were examined. Using these metrics, the tracks were classified into four behavior categories, described herein as Directed Travel, Repeated Stationary Dives, Mill, and tracks with Combinations of behavioral states. Some diel and seasonal patterns were identified, with Mill tracks occurring more at night than the other behaviors, Repeated Stationary Dive tracks occurring more during the day, and Directed Travel occurring only at the start and end of the breeding season. These results provide detailed insights into the movement of singing humpback whales, particularly in offshore waters where they may be migrating into or out of breeding grounds. This also contributes valuable information on the baseline behavior of humpback whales on a US Navy training range.