iDNA from terrestrial haematophagous leeches as a wildlife surveying and monitoring tool - prospects, pitfalls and avenues to be developed

Invertebrate-derived DNA (iDNA) from terrestrial haematophagous leeches has recently been proposed as a powerful non-invasive tool with which to detect vertebrate species and thus to survey their populations. However, to date little attention has been given to whether and how this, or indeed any other iDNA-derived data, can be combined with state-of-the-art analytical tools to estimate wildlife abundances, population dynamics and distributions. In this review, we discuss the challenges that face the application of existing analytical methods such as site-occupancy and spatial capture-recapture (SCR) models to terrestrial leech iDNA, in particular, possible violations of key assumptions arising from factors intrinsic to invertebrate parasite biology. Specifically, we review the advantages and disadvantages of terrestrial leeches as a source of iDNA and summarize the utility of leeches for presence, occupancy, and spatial capture-recapture models. The main source of uncertainty that attends species detections derived from leech gut contents is attributable to uncertainty about the spatio-temporal sampling frame, since leeches retain host-blood for months and can move after feeding. Subsequently, we briefly address how the analytical challenges associated with leeches may apply to other sources of iDNA. Our review highlights that despite the considerable potential of leech (and indeed any) iDNA as a new survey tool, further pilot studies are needed to assess how analytical methods can overcome or not the potential biases and assumption violations of the new field of iDNA. Specifically we argue that studies to compare iDNA sampling with standard survey methods such as camera trapping, and those to improve our knowledge on leech (and other invertebrate parasite) physiology, taxonomy, and ecology will be of immense future value

Immune DNA signature of T-cell infiltration in breast tumor exomes.

Tumor infiltrating lymphocytes (TILs) have been associated with favorable prognosis in multiple tumor types. The Cancer Genome Atlas (TCGA) represents the largest collection of cancer molecular data, but lacks detailed information about the immune environment. Here, we show that exome reads mapping to the complementarity-determining-region 3 (CDR3) of mature T-cell receptor beta (TCRB) can be used as an immune DNA (iDNA) signature. Specifically, we propose a method to identify CDR3 reads in a breast tumor exome and validate it using deep TCRB sequencing. In 1,078 TCGA breast cancer exomes, the fraction of CDR3 reads was associated with TILs fraction, tumor purity, adaptive immunity gene expression signatures and improved survival in Her2+ patients. Only 2/839 TCRB clonotypes were shared between patients and none associated with a specific HLA allele or somatic driver mutations. The iDNA biomarker enriches the comprehensive dataset collected through TCGA, revealing associations with other molecular features and clinical outcomes

Archeota, Spring 2018

https://scholarworks.sjsu.edu/saasc_archeota/1007/thumbnail.jp

Bloodlines: mammals, leeches, and conservation in southern Asia

Southern Asia is a biodiversity hotspot both for terrestrial mammals and for leeches. Many small-mammal groups are under-studied in this region, while other mammals are of known conservation concern. In addition to standard methods for surveying mammals, it has recently been demonstrated that residual bloodmeals within leeches can be sequenced to find mammals in a given area. While these invertebrate-parasite-derived DNA (iDNA) methods are promising, most of the leech species utilized for this type of survey remain unevaluated, notwithstanding that their diversity varies substantially. Here we examine approximately 750 individual leech specimens in the genus Haemadipsa across a large range in southern Asia (Bangladesh, Cambodia, and China), specifically reviewing the diversity of mammals they feed on and their own genetic structuring. Leeches were found to feed on a considerable variety of mammals, corroborating prior studies. Additionally, leeches were found to have fed both on bats and on birds, neither of which has previously been recorded with this method. The genetic structuring of the leeches themselves revealed 15 distinct clades of which only two precisely corresponded to previously characterized species, indicating that much work is needed to finalize classifications in this genus. Most importantly, with regards to mammal conservation, leeches in these clades appear to feed on a broad range of mammals

Quantization of four-dimensional Abelian gravity

An abelian version of standard general relativity in the Cartan-Palatini gauge-like formulation in four dimensions has been introduced. Traditional canonical analysis utilizing similarities to the akin Husain-Kuchar SU(2) version of gravity has been performed. The model has been next quantized in the canonical path-integral Faddeev-Popov formalism yielding abelian BF theory.Comment: Minor changes, additional symmetry discussed. 5 pages, 2 columns, REVTeX

Novel Bacterial Diversity and Fragmented eDNA Identified in Hyperbiofilm-Forming Pseudomonas aeruginosa Rugose Small Colony Variant

Pseudomonas aeruginosa biofilms represent a major threat to health care. Rugose small colony variants (RSCV) of P. aeruginosa, isolated from chronic infections, display hyperbiofilm phenotype. RSCV biofilms are highly resistant to antibiotics and host defenses. This work shows that RSCV biofilm aggregates consist of two distinct bacterial subpopulations that are uniquely organized displaying contrasting physiological characteristics. Compared with that of PAO1, the extracellular polymeric substance of RSCV PAO1ΔwspF biofilms presented unique ultrastructural characteristics. Unlike PAO1, PAO1ΔwspF released fragmented extracellular DNA (eDNA) from live cells. Fragmented eDNA, thus released, was responsible for resistance of PAO1ΔwspF biofilm to disruption by DNaseI. When added to PAO1, such fragmented eDNA enhanced biofilm formation. Disruption of PAO1ΔwspF biofilm was achieved by aurine tricarboxylic acid, an inhibitor of DNA-protein interaction. This work provides critical novel insights into the contrasting structural and functional characteristics of a hyperbiofilm-forming clinical bacterial variant relative to its own wild-type strain

More efficient Bell inequalities for Werner states

In this paper we study the nonlocal properties of two-qubit Werner states parameterized by the visibility parameter 0<p<1. New family of Bell inequalities are constructed which prove the two-qubit Werner states to be nonlocal for the parameter range 0.7056<p<1. This is slightly wider than the range 0.7071<p<1, corresponding to the violation of the Clauser-Horne-Shimony-Holt (CHSH) inequality. This answers a question posed by Gisin in the positive, i.e., there exist Bell inequalities which are more efficient than the CHSH inequality in the sense that they are violated by a wider range of two-qubit Werner states.Comment: 7 pages, 1 figur

Detection and Analysis of Antibiotic Resistance Genes in a Wastewater Treatment Process

目前，随着在越来越多的污水样品和处理后的生物残渣中检测到耐药菌和抗性基因，人们已逐渐认识到污水处理厂是这二者的一个主要容留场所。环境中的这些抗性基因可以作为感染源水平转移到人类机体微生物中，也因此导致了抗生素耐药性的扩大化。由于胞外基因分子可以在水环境中保持相当长时间的生物活性，而目前关于污水中胞外基因的报道甚少，本文将着重调查典型的污水处理工艺——膜生物反应器中的胞外基因，并在此基础上进一步考察膜生物反应器出水中的胞外抗性基因（尤其是磺胺甲恶唑抗性基因）可能对细菌产生的抗性基因转化。 首先，本文改进和验证了一项同时提取胞内和胞外基因的方法，结果显示胞外基因的回收率为43-67%且几乎没有细...Nowadays, wastewater treatment plants have been gradually recognized as a reservoir for antibiotic resistant bacteria and antibiotic resistance genes(ARGs), which were found in lots of wastewater samples and treated biosolids. These environmental ARGs then could serve as a source and be horizontally transferred to human-associated bacteria and thus contribute to antibiotic resistance proliferation...学位：工学硕士院系专业：化学化工学院_化学工程学号：2042012115417

Transitory Microbial Habitat in the Hyperarid Atacama Desert

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: a physico-chemical characterization of the soil habitability after an exceptional rain event, identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity. [Abstract copyright: Copyright © 2018 the Author(s). Published by PNAS.

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