追访越境者

写这篇文字的时候,我一直在想．是什么使这些纯朴本分的农民,变成了一群甘愿以身试法的越境者？     

Estimating the Location and Spatial Extent of a Covert Anthrax Release

Rapidly identifying the features of a covert release of an agent such as anthrax could help to inform the planning of public health mitigation strategies. Previous studies have sought to estimate the time and size of a bioterror attack based on the symptomatic onset dates of early cases. We extend the scope of these methods by proposing a method for characterizing the time, strength, and also the location of an aerosolized pathogen release. A back-calculation method is developed allowing the characterization of the release based on the data on the first few observed cases of the subsequent outbreak, meteorological data, population densities, and data on population travel patterns. We evaluate this method on small simulated anthrax outbreaks (about 25–35 cases) and show that it could date and localize a release after a few cases have been observed, although misspecifications of the spore dispersion model, or the within-host dynamics model, on which the method relies can bias the estimates. Our method could also provide an estimate of the outbreak's geographical extent and, as a consequence, could help to identify populations at risk and, therefore, requiring prophylactic treatment. Our analysis demonstrates that while estimates based on the first ten or 15 observed cases were more accurate and less sensitive to model misspecifications than those based on five cases, overall mortality is minimized by targeting prophylactic treatment early on the basis of estimates made using data on the first five cases. The method we propose could provide early estimates of the time, strength, and location of an aerosolized anthrax release and the geographical extent of the subsequent outbreak. In addition, estimates of release features could be used to parameterize more detailed models allowing the simulation of control strategies and intervention logistics.     

A Mixed-Method Approach for Quantifying Illegal Fishing and Its Impact on an Endangered Fish Species

Illegal harvest is recognized as a widespread problem in natural resource management. The use of multiple methods for quantifying illegal harvest has been widely recommended yet infrequently applied. We used a mixed-method approach to evaluate the extent, character, and motivations of illegal gillnet fishing in Lake Hovsgol National Park, Mongolia and its impact on the lake’s fish populations, especially that of the endangered endemic Hovsgol grayling (Thymallus nigrescens). Surveys for derelict fishing gear indicate that gillnet fishing is widespread and increasing and that fishers generally use 3–4 cm mesh gillnet. Interviews with resident herders and park rangers suggest that many residents fish for subsistence during the spring grayling spawning migration and that some residents fish commercially year-round. Interviewed herders and rangers generally agree that fish population sizes are decreasing but are divided on the causes and solutions. Biological monitoring indicates that the gillnet mesh sizes used by fishers efficiently target Hovsgol grayling. Of the five species sampled in the monitoring program, only burbot (Lota lota) showed a significant decrease in population abundance from 2009–2013. However, grayling, burbot, and roach (Rutilus rutilus) all showed significant declines in average body size, suggesting a negative fishing impact. Data-poor stock assessment methods suggest that the fishing effort equivalent to each resident family fishing 50-m of gillnet 11–15 nights per year would be sufficient to overexploit the grayling population. Results from the derelict fishing gear survey and interviews suggest that this level of effort is not implausible. Overall, we demonstrate the ability for a mixed-method approach to effectively describe an illegal fishery and suggest that these methods be used to assess illegal fishing and its impacts in other protected areas.     

Derelict Fishing Line Provides a Useful Proxy for Estimating Levels of Non-Compliance with No-Take Marine Reserves

No-take marine reserves (NTMRs) are increasingly being established to conserve or restore biodiversity and to enhance the sustainability of fisheries. Although effectively designed and protected NTMR networks can yield conservation and fishery benefits, reserve effects often fail to manifest in systems where there are high levels of non-compliance by fishers (poaching). Obtaining reliable estimates of NTMR non-compliance can be expensive and logistically challenging, particularly in areas with limited or non-existent resources for conducting surveillance and enforcement. Here we assess the utility of density estimates and re-accumulation rates of derelict (lost and abandoned) fishing line as a proxy for fishing effort and NTMR non-compliance on fringing coral reefs in three island groups of the Great Barrier Reef Marine Park (GBRMP), Australia. Densities of derelict fishing line were consistently lower on reefs within old (>20 year) NTMRs than on non-NTMR reefs (significantly in the Palm and Whitsunday Islands), whereas line densities did not differ significantly between reefs in new NTMRs (5 years of protection) and non-NTMR reefs. A manipulative experiment in which derelict fishing lines were removed from a subset of the monitoring sites demonstrated that lines re-accumulated on NTMR reefs at approximately one third (32.4%) of the rate observed on non-NTMR reefs over a thirty-two month period. Although these inshore NTMRs have long been considered some of the best protected within the GBRMP, evidence presented here suggests that the level of non-compliance with NTMR regulations is higher than previously assumed.     

从“瓢舀鱼”到越境捕捞

直接从自然索取,采摘、狩猎、捕鱼、放牧等等,是人类在地球上成本最低的生存方式,以致在一切可能地方至今还在延续着。可悲的是．这样的方式在许多地方因为过度地索取而没能持久下去。人们怎样才能在失去这种方式之前就能够意识到从自然的索取是有限度的,成了能否低成本地与自然保持和谐的关键。     

Worldwide genetic analysis of the CFTR region

Mutations at the cystic fibrosis transmembrane conductance regulator gene (CFTR) cause cystic fibrosis, the most prevalent severe genetic disorder in individuals of European descent. We have analyzed normal allele and haplotype variation at four short tandem repeat polymorphisms (STRPs) and two single-nucleotide polymorphisms (SNPs) in CFTR in 18 worldwide population samples, comprising a total of 1,944 chromosomes. The rooted phylogeny of the SNP haplotypes was established by typing ape samples. STRP variation within SNP haplotype backgrounds was highest in most ancestral haplotypes-although, when STRP allele sizes were taken into account, differences among haplotypes became smaller. Haplotype background determines STRP diversity to a greater extent than populations do, which indicates that haplotype backgrounds are older than populations. Heterogeneity among STRPs can be understood as the outcome of differences in mutation rate and pattern. STRP sites had higher heterozygosities in Africans, although, when whole haplotypes were considered, no significant differences remained. Linkage disequilibrium (LD) shows a complex pattern not easily related to physical distance. The analysis of the fraction of possible different haplotypes not found may circumvent some of the methodological difficulties of LD measure. LD analysis showed a positive correlation with locus polymorphism, which could partly explain the unusual pattern of similar LD between Africans and non-Africans. The low values found in non-Africans may imply that the size of the modern human population that emerged "Out of Africa" may be larger than what previous LD studies suggested.     

Fishing the molecular bases of Treacher Collins syndrome

Treacher Collins syndrome (TCS) is an autosomal dominant disorder of craniofacial development, and mutations in the TCOF1 gene are responsible for over 90% of TCS cases. The knowledge about the molecular mechanisms responsible for this syndrome is relatively scant, probably due to the difficulty of reproducing the pathology in experimental animals. Zebrafish is an emerging model for human disease studies, and we therefore assessed it as a model for studying TCS. We identified in silico the putative zebrafish TCOF1 ortholog and cloned the corresponding cDNA. The derived polypeptide shares the main structural domains found in mammals and amphibians. Tcof1 expression is restricted to the anterior-most regions of zebrafish developing embryos, similar to what happens in mouse embryos. Tcof1 loss-of-function resulted in fish showing phenotypes similar to those observed in TCS patients, and enabled a further characterization of the mechanisms underlying craniofacial malformation. Besides, we initiated the identification of potential molecular targets of treacle in zebrafish. We found that Tcof1 loss-of-function led to a decrease in the expression of cellular proliferation and craniofacial development. Together, results presented here strongly suggest that it is possible to achieve fish with TCS-like phenotype by knocking down the expression of the TCOF1 ortholog in zebrafish. This experimental condition may facilitate the study of the disease etiology during embryonic development.     

On the Extent of Tyrosine Phosphorylation in Chloroplasts

Reanalysis of published mass spectrometry data on Tyr-phosphorylated chloroplast proteins indicates that the majority of peptide spectrum matches reporting Tyr phosphorylation are ambiguous.Tyr phosphorylation is a controversial issue in plant phosphoproteomics, ever since early analyses reported up to 5% Tyr phosphorylation in Arabidopsis (Arabidopsis thaliana), despite the lack of a classical Tyr kinase in the Arabidopsis genome (Sugiyama et al., 2008; de la Fuente van Bentem and Hirt, 2009). The same controversy extends to the phosphorylation of chloroplast proteins. In the past 20 years, several indications for Tyr phosphorylation in chloroplasts were reported, and Rubisco is annotated as Tyr phosphorylated protein (www.arabidopsis.org). Initially, Tullberg et al. (1998) found the protein Tyr kinase inhibitor genistein to inhibit the phosphorylation of thylakoid membrane proteins. Supported by the observed stability of some thylakoid phosphoproteins against acid and base hydrolysis, a characteristic property of phospho-Tyr, the authors argue that Tyr phosphorylation of thylakoid membrane proteins is vital for short-term acclimation responses. Similar biochemical properties were observed for autophosphorylation of the chloroplast sensor kinase CSK (Puthiyaveetil et al., 2008). Support for Tyr phosphorylation came from the cross-reactivity of thylakoid membrane proteins and Calvin cycle enzymes (e.g. Rubisco) with phospho-Tyr-specific antibodies (Forsberg and Allen, 2001; Fedina et al., 2008; Ghelis et al., 2008). With the same set of methods, no Tyr phosphorylation was observed in mitochondrial proteins (Forsberg and Allen, 2001).The above reported data are indirect hints for Tyr phosphorylation, and none of the applied methods is sufficiently specific to serve as solid evidence. For example, all phospho-Tyr-specific antibodies have significant cross reactivity with phospho-Ser and phospho-Thr when these have an aromatic amino acid in the +1 position (Zerweck et al., 2009). Using phospho-Tyr-specific antibodies, Forsberg and Allen (2001) found genistein inhibition of light-harvesting complex II phosphorylation with a 50% inhibition of initial activity of around 15 µm. Surprisingly, the same inhibition kinetics were observed with phospho-Thr-specific antibodies, suggesting a lack of specificity of either genistein or the phospho-amino acid antibodies, or both. So far, direct proof for Tyr phosphorylation in chloroplasts by phospho-amino acid analyses is missing. However, mass spectrometry-based phosphoproteomics experiments with plant cell extracts reported phospho-Tyr-containing peptides in chloroplasts but surprisingly not in abundant thylakoid membrane proteins or Calvin cycle enzymes. A recent meta-analysis collated data from 27 published studies and several internal data sets, resulting in a cumulative data set with 5% Tyr-phosphorylated peptides in the entire data set and 12% to 19% in the mitochondria (van Wijk et al., 2014). In this data set, almost 30% of the plastid phosphoproteins are flagged as Tyr phosphorylated (90 proteins from around 300; see supplemental table 5B in van Wijk et al., 2014), standing in stark contrast to dedicated plastid phosphoproteome analyses that identified less than 1% Tyr phosphorylation in the cellular phosphoproteome and none in chloroplast proteins (Reiland et al., 2009).Many of the phospho-Tyr-containing peptides were identified in analyses that applied multistage activation to elevate fragment ion intensity in spectra dominated by the neutral loss of phosphoric acid from phospho-Ser and/or phospho-Thr, sometimes in combination with searches for the phospho-Tyr-specific immonium ion at mass-to-charge ratio 216.0426 (see table 1 in van Wijk et al., 2014). In one instance, phospho-Tyr-specific antibodies were used to enrich Tyr phosphorylated proteins from Arabidopsis full cell extracts (Mithoe et al., 2012). Remarkably, there is almost no overlap in phospho-Tyr peptide identification between the different studies (Mithoe et al., 2012; Wu et al., 2013; van Wijk et al., 2014). Although this could be the result of diverse acquisition methods, enrichment strategies, and data interpretation software in different analyses (Bodenmiller et al., 2007), the low reproducibility and the discrepancies in phospho-Tyr detection among different analyses require further attention, because both are characteristic for incorrect peptide spectrum matches. This is a specific problem here, because false discovery rates (FDRs) accumulate in cumulated data sets.Therefore, we decided to assess the quality of matches to Tyr phosphorylated peptides by a dedicated reanalysis of the original data and benchmarked the robustness of peptide identification by using different software tools for spectra interpretation. Different tools use different scoring schemes to calculate identification probabilities from the fragment ion spectrum; however, they all use basic rules for spectrum matching, such as consecutive b- or y-ion series, matching of the highest intensity peaks to peptide fragments, and identification of matches to plausible derivatives of the major fragments such as losses of ammonia or water. Because of the differences in scoring the identified fragment ions, software tools may interpret spectra differently. However, since the basic rules for peptide matching apply to all identifications, it is clear that robust and reliable identifications are made by different tools that agree on the same interpretation for a spectrum. A specific aspect in the interpretation of phosphopeptide spectra is the assignment of the exact modification site. Common database matching software is usually unsuitable to distinguish modifications at closely spaced amino acids, and it is insufficiently explicit when spectra do not allow distinguishing between alternatives. To circumvent this problem, specialized software tools were developed that score spectra for alternative phosphorylation sites within the peptide sequence by searching for specific fragment ions supporting one or another phosphorylation site (MacLean et al., 2008; Martin et al., 2010).We extracted from the different data sets Tyr-phosphorylated chloroplast proteins and extracted the spectrum information in the form of a MASCOT generic file (mgf) from either PhosphAT (van Wijk et al., 2014) or PRIDE (Mithoe et al., 2012). This resulted in 139 spectra identifying 53 unique peptides representing putative Tyr phosphorylation sites in 53 chloroplast proteins (Supplemental Table S1A; Supplemental Data Set S1). This set of spectra was reanalyzed with MASCOT to assess the significance of the identifications and two alternative software tools established for database searches: PEAKS, a database matching software with a de novo sequencing option (Ma et al., 2003); and Proteome Discoverer with the search engine SEQUEST (Thermo Scientific). With the original search parameters of dynamic phosphorylation of Ser, Thr, and Tyr, dynamic oxidation of Met, fixed carbamidomethylation of Cys, and maximum of two missed cleavages at mass tolerances for precursor and fragment ion matching of 20 ppm/0.5 D (Wu et al., 2013), 50 ppm/0.8 D (internal data sets in van Wijk et al., 2014), and 10 ppm/0.9 D (Mithoe et al., 2012), 11 out of 53 unique peptides were identified with the reported amino acid sequence above the MASCOT significance threshold of P < 0.05, while 42 mgf matchings were reported as insignificant or gave rise to an unrelated peptide identification (www.matrixscience.com; Supplemental Table S1B). The lack of significance correlates with the relaxed search parameters and the many degrees of freedom allowed for peptide matching. With a variation of the above mass tolerance settings, PEAKS identified five (9%) and Proteome Discoverer identified 11 (21%) out of 53 peptides from the data set at a fully relaxed FDR, of which three (6%) identifications by PEAKS and one (2%) by Proteome Discoverer were significant (van Wijk et al., 2014)Presented are those peptides that were identified at least once with one of the alternative tools at one of the indicated mass tolerance settings: precursor tolerance/tandem mass spectrometry/ion match tolerance 50 ppm/0.8 D, 20 ppm/0.5 D, or 10 ppm/0.9 D. We reported all identifications irrespective of the score. Identifications considered significant are labeled with asterisks. Provided is the FDR at which the identification was made. Proteome Discoverer has two FDR settings: below 1% (stringent) or below 5% (relaxed). All matches above a 5% FDR threshold are considered insignificant. The PEAKS FDR is calculated individually for every peptide. Dashes indicate that the peptide was not identified.