Comprehensive criteria for biodiversity evaluation in conservation planning

In this paper we present the results of a multi-criteria decision analysis used to identify a comprehensive set of criteria for assigning biodiversity value to sites for conservation planning. For effective conservation management, biodiversity value needs to be a composite of biotic and abiotic factors. However, in the reserve design literature, conservation value is assigned with a limited set of metrics usually based on comprehensiveness, representativeness and persistence which may be insufficient at fully capturing biodiversity value. A group of conservation specialists in California, USA, used a multi-criteria decision making framework to elucidate and weight criteria for scoring biodiversity value at sites. A formal model for consensus and negotiation was applied to aggregate individuals’ criteria weights across all group members. The group identified ecological condition, followed by biotic composition as the most important contributors to site conservation value. Long- and short-term threats causing fragmentation and degradation are also important criteria to consider. Key criteria are identified for which further data collection would serve the greatest purpose in prioritizing sites and the role of prioritization criteria in the larger context of systematic conservation planning is discussed. With the recognition that biodiversity value plays an important role in conservation decisions, the criteria presented here represents a comprehensive suite of factors to consider when assigning biodiversity value to sites for conservation planning. These can serve as an encompassing list which other groups can customize for the purpose of biodiversity evaluation for alternative conservation planning contexts.     

Defective i6A37 Modification of Mitochondrial and Cytosolic tRNAs Results from Pathogenic Mutations in TRIT1 and Its Substrate tRNA

Identifying the genetic basis for mitochondrial diseases is technically challenging given the size of the mitochondrial proteome and the heterogeneity of disease presentations. Using next-generation exome sequencing, we identified in a patient with severe combined mitochondrial respiratory chain defects and corresponding perturbation in mitochondrial protein synthesis, a homozygous p.Arg323Gln mutation in TRIT1. This gene encodes human tRNA isopentenyltransferase, which is responsible for i⁶A37 modification of the anticodon loops of a small subset of cytosolic and mitochondrial tRNAs. Deficiency of i⁶A37 was previously shown in yeast to decrease translational efficiency and fidelity in a codon-specific manner. Modelling of the p.Arg323Gln mutation on the co-crystal structure of the homologous yeast isopentenyltransferase bound to a substrate tRNA, indicates that it is one of a series of adjacent basic side chains that interact with the tRNA backbone of the anticodon stem, somewhat removed from the catalytic center. We show that patient cells bearing the p.Arg323Gln TRIT1 mutation are severely deficient in i⁶A37 in both cytosolic and mitochondrial tRNAs. Complete complementation of the i⁶A37 deficiency of both cytosolic and mitochondrial tRNAs was achieved by transduction of patient fibroblasts with wild-type TRIT1. Moreover, we show that a previously-reported pathogenic m.7480A>G mt-tRNA^Ser(UCN) mutation in the anticodon loop sequence A36A37A38 recognised by TRIT1 causes a loss of i⁶A37 modification. These data demonstrate that deficiencies of i⁶A37 tRNA modification should be considered a potential mechanism of human disease caused by both nuclear gene and mitochondrial DNA mutations while providing insight into the structure and function of TRIT1 in the modification of cytosolic and mitochondrial tRNAs.     

gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair

The widespread use of Next Generation Sequencing has opened up new avenues for cancer research and diagnosis. NGS will bring huge amounts of new data on cancer, and especially cancer genetics. Current knowledge and future discoveries will make it necessary to study a huge number of genes that could be involved in a genetic predisposition to cancer. In this regard, we developed a Nextera design to study 11 complete genes involved in DNA damage repair. This protocol was developed to safely study 11 genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CHEK2, PALB2, RAD50, RAD51C, RAD80, and TP53) from promoter to 3''-UTR in 24 patients simultaneously. This protocol, based on transposase technology and gDNA enrichment, gives a great advantage in terms of time for the genetic diagnosis thanks to sample multiplexing. This protocol can be safely used with blood gDNA.     

The Effect of Neoadjuvant Chemoradiotherapy on Whole-Body Physical Fitness and Skeletal Muscle Mitochondrial Oxidative Phosphorylation In Vivo in Locally Advanced Rectal Cancer Patients – An Observational Pilot Study

Background

In the United Kingdom, patients with locally advanced rectal cancer routinely receive neoadjuvant chemoradiotherapy. However, the effects of this on physical fitness are unclear. This pilot study is aimed to investigate the effect of neoadjuvant chemoradiotherapy on objectively measured in vivo muscle mitochondrial function and whole-body physical fitness.

Methods

We prospectively studied 12 patients with rectal cancer who completed standardized neoadjuvant chemoradiotherapy, recruited from a large tertiary cancer centre, between October 2012 and July 2013. All patients underwent a cardiopulmonary exercise test and a phosphorus magnetic resonance spectroscopy quadriceps muscle exercise-recovery study before and after neoadjuvant chemoradiotherapy. Data were analysed and reported blind to patient identity and clinical course. Primary variables of interest were the two physical fitness measures; oxygen uptake at estimated anaerobic threshold and oxygen uptake at Peak exercise (ml.kg⁻¹.min⁻¹), and the post-exercise phosphocreatine recovery rate constant (min⁻¹), a measure of muscle mitochondrial capacity in vivo.

Results

Median age was 67 years (IQR 64–75). Differences (95%CI) in all three primary variables were significantly negative post-NACRT: Oxygen uptake at estimated anaerobic threshold −2.4 ml.kg⁻¹.min⁻¹ (−3.8, −0.9), p = 0.004; Oxygen uptake at Peak −4.0 ml.kg⁻¹.min⁻¹ (−6.8, −1.1), p = 0.011; and post-exercise phosphocreatine recovery rate constant −0.34 min⁻¹ (−0.51, −0.17), p<0.001.

Conclusion

The significant decrease in both whole-body physical fitness and in vivo muscle mitochondrial function raises the possibility that muscle mitochondrial mechanisms, no doubt multifactorial, may be important in deterioration of physical fitness following neoadjuvant chemoradiotherapy. This may have implications for targeted interventions to improve physical fitness pre-surgery.

Trial Registration

Clinicaltrials.gov registration {"type":"clinical-trial","attrs":{"text":"NCT01859442","term_id":"NCT01859442"}}NCT01859442     

Inorganic nitrogen uptake kinetics of sugarcane (Saccharum spp.) varieties under in vitro conditions with varying N supply

An in vitro system was established for the characterisation of inorganic nitrogen uptake by sugarcane plantlets of variety NCo376. After multiplication and rooting, plantlets (0.27–0.3 g fresh mass) were placed on N-free medium for 4 days, and then supplied with 2–20 mM N as NO₃ ^?-N only, NH₄ ⁺-N only or NO₃ ^?-N + NH₄ ⁺-N (as 1:1). With few exceptions, on all the tested N media, the in vitro plants always had a higher V_max for NH₄ ⁺-N (28.69–66.51 μmol g^?1 h^?1) than for NO₃ ^?-N uptake (10.24–30.19 μmol g^?1 h^?1) and the K_m indicated a higher affinity for NO₃ ^?-N (0.02–7.38 mM) than for NH₄ ⁺-N (0.06–9.15 mM). When N was applied as 4 and 20 mM to varieties N12, N19 and N36, the interaction between variety, N form and concentration resulted in differences in the V_max and K_m. The high N-use efficient varieties (N12 and N19), as determined in previous pot and field trials, behaved similarly under all tested conditions and displayed a lower V_max and K_m than the low N-use efficient ones (NCo376 and N36). Based on this finding, it was suggested that the N-use efficient designation (from pot and field trials) may not be ascribed solely to N uptake. Assessment of the relative preference index (RPI) for NO₃ ^?-N and NH₄ ⁺-N uptake revealed that, at present, the RPI has no application in sugarcane due to its preferential uptake of NH₄ ⁺-N.     

Defective immunogenic cell death of HMGB1-deficient tumors: compensatory therapy with TLR4 agonists

Immunogenic cell death induced by anticancer chemotherapy is characterized by a series of molecular hallmarks that include the exodus of high-mobility group box 1 protein (HMGB1) from dying cells. HMGB1 is a nuclear nonhistone chromatin-binding protein. It is secreted at the late stages of cellular demise and engages Toll-like receptor4 (TLR4) on dendritic cells (DCs) to accelerate the processing of phagocytic cargo in the DC and to facilitate antigen presentation by DC to T cells. The absence of HMGB1 expression by dying tumor cells exposed to anthracyclines or oxaliplatin compromises DC-dependent T-cell priming by tumor-associated antigens. Here, we show that transplantable tumors exhibiting weak expression of nuclear HMGB1 respond to chemotherapy more effectively if the treatment is combined with the local or systemic administration of a highly purified and physiochemically defined and standardized lipopolysaccharide solution, which acts as a high-potency and exclusive TLR4 agonist, called Dendrophilin (DEN). The synergistic antitumor effects mediated by the combination of chemotherapy and immunotherapy relied upon the presence of the MyD88 (myeloid differentiation primary response gene) adapter of TLR4 (but not that of the TIR-domain-containing adapter-inducing interferon-β adapter), in line with the well-characterized action of DEN on the MyD88 signaling pathway. DEN and anthracyclines synergized to induce intratumoral accumulation of interferon-γ-producing CD4⁺ and CD8⁺ T lymphocytes. Moreover, DEN could restore the immunogenicity of dying tumor cells from which HMGB1 had been depleted by RNA interference. These findings underscore the potential clinical utility of combination regimens involving immunogenic chemotherapy and certain TLR4 agonists in advanced HMGB1-deficient cancers.     

openPDS: Protecting the Privacy of Metadata through SafeAnswers

The rise of smartphones and web services made possible the large-scale collection of personal metadata. Information about individuals'' location, phone call logs, or web-searches, is collected and used intensively by organizations and big data researchers. Metadata has however yet to realize its full potential. Privacy and legal concerns, as well as the lack of technical solutions for personal metadata management is preventing metadata from being shared and reconciled under the control of the individual. This lack of access and control is furthermore fueling growing concerns, as it prevents individuals from understanding and managing the risks associated with the collection and use of their data. Our contribution is two-fold: (1) we describe openPDS, a personal metadata management framework that allows individuals to collect, store, and give fine-grained access to their metadata to third parties. It has been implemented in two field studies; (2) we introduce and analyze SafeAnswers, a new and practical way of protecting the privacy of metadata at an individual level. SafeAnswers turns a hard anonymization problem into a more tractable security one. It allows services to ask questions whose answers are calculated against the metadata instead of trying to anonymize individuals'' metadata. The dimensionality of the data shared with the services is reduced from high-dimensional metadata to low-dimensional answers that are less likely to be re-identifiable and to contain sensitive information. These answers can then be directly shared individually or in aggregate. openPDS and SafeAnswers provide a new way of dynamically protecting personal metadata, thereby supporting the creation of smart data-driven services and data science research.     

Dysfunctional telomeres induce p53‐dependent and independent apoptosis to compromise cellular proliferation and inhibit tumor formation

Aging is associated with progressive telomere shortening, resulting in the formation of dysfunctional telomeres that compromise tissue proliferation. However, dysfunctional telomeres can limit tumorigenesis by activating p53‐dependent cellular senescence and apoptosis. While activation of both senescence and apoptosis is required for repress tumor formation, it is not clear which pathway is the major tumor suppressive pathway in vivo. In this study, we generated Eμ‐myc; Pot1b ^?/? mouse to directly compare tumor formation under conditions in which either p53‐dependent apoptosis or senescence is activated by telomeres devoid of the shelterin component Pot1b. We found that activation of p53‐dependent apoptosis plays a more critical role in suppressing lymphoma formation than p53‐dependent senescence. In addition, we found that telomeres in Pot1b^?/?; p53^?/? mice activate an ATR‐Chk1‐dependent DNA damage response to initiate a robust p53‐independent, p73‐dependent apoptotic pathway that limited stem cell proliferation but suppressed B‐cell lymphomagenesis. Our results demonstrate that in mouse models, both p53‐dependent and p53‐independent apoptosis are important to suppressing tumor formation.     

Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria

The diversity of bacterial species in the human oral cavity is well recognized, but a high proportion of them are presently uncultivable. Candidate division TM7 bacteria are almost always detected in metagenomic studies but have not yet been cultivated. In this paper, we identified candidate division TM7 bacterial phylotypes in mature plaque samples from around orthodontic bonds in subjects undergoing orthodontic treatment. Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes. The bacteria formed filaments of 20 to 200 μm in length within agar plate colonies and in monospecies biofilms on salivary pellicle and exhibited some unusual morphological characteristics by transmission electron microscopy, including a trilaminated cell surface layer and dense cytoplasmic deposits. Proteomic analyses of cell wall protein extracts identified abundant polypeptides predicted from the TM7 partial genomic sequence. Pleiomorphic phenotypes were observed when the candidate division TM7 bacterium was grown in dual-species biofilms with representatives of six different oral bacterial genera. The TM7 bacterium formed long filaments in dual-species biofilm communities with Actinomyces oris or Fusobacterium nucleatum. However, the TM7 isolate grew as short rods or cocci in dual-species biofilms with Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, or Streptococcus gordonii, forming notably robust biofilms with the latter two species. The ability to cultivate TM7 axenically should majorly advance understanding of the physiology, genetics, and virulence properties of this novel candidate division oral bacterium.     

Safety testing of metabolites: Expectations and outcomes

Metabolites arising from chemical entities, old or new, are often mediators of toxicity. Frequently, metabolites are investigated in test animals, with the expectation that the resultant toxicity or activity will mimic the exposure of their formed counterparts. This communication described observations that showed discrepant kinetics between formed and preformed metabolites in the liver, intestine, and kidney, major drug removal organs. Differences in the observed areas under the curve (AUCs) or the extraction ratios (Es) of formed and preformed metabolites in the liver had been attributed to zonal, enzyme heterogeneity, membrane barriers, or transporters. Preformed and formed metabolite also differed in their handling by the kidney; only the preformed and not the formed metabolite would be filtered. In the intestine, differences in the absorption of the precursor and the metabolite and the flow pattern in the intestine would bring about discrepancy in the time-courses of the formed vs. preformed metabolites. Analytical solutions of the AUCs of the metabolites and extraction ratios, based on physiological modeling of the liver, kidney, and intestine, showed that the AUC of the preformed, administered metabolite was dependent only on metabolite parameters, whereas the AUC of the formed metabolite was modulated additionally by the metabolic, secretory and intestinal absorptive intrinsic clearances of the precursor drug. Hence, administration of the synthetic metabolite would not reflect the toxicity associated with the metabolite formed via bioactivation. However, data on preformed metabolite may be used for simultaneous fitting by a combined model of drug and metabolite. Such a strategy is shown to be successful in risk assessment of environmental chemicals. Upon refinement of the resultant model with data on metabolite transport and handling by modeling and simulations, the resultant model would be more robust to provide improved predictions on metabolite toxicity pursuant to drug administration.