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At least 127 records · Page 7

Ecological connectivity and habitat loss shape patterns of genetic diversity in a threatened salamander

Context The maintenance of genetic diversity is essential for preserving adaptive potential in populations, yet it is increasingly threatened by landscape alteration. The field of landscape genetics offers a framework for assessing how patch-level landscape conditions, modeled at multiple scales, influence genetic diversity. Objectives We sought to assess how local environmental features and connectivity influence genetic diversity across 74 four-toed salamander (Hemidactylium scutatum) breeding wetlands in the southeastern United States. Methods Using next-generation sequencing data and hierarchical Bayesian models, we examined genome-wide heterozygosity in relation to local landscape features and ecological connectivity. We also assessed the scale of effect of landscape features and tested for temporal lag effects. Results Genetic diversity was lower in wetlands with higher levels of historic deforestation and lower connectivity. An interaction between deforestation and connectivity indicated that deforestation had stronger negative effects in isolated wetlands but weaker effects in well-connected wetlands. Accounting for scale of effect and temporal lags was critical for detecting these relationships. Conclusions Our analyses highlight the importance of assessing the spatial scale (scale of effect) and temporal lag of landscape features to detect key drivers of genetic diversity. In line with population genetic theory, our results indicate that the genetic consequences of habitat loss do not affect populations uniformly and are most severe in isolated populations where gene flow cannot buffer against loss of diversity. Altogether, we highlight the importance of considering the interaction of habitat loss and connectivity in conservation genetic management.

Hemidactylium scutatum↗

Genetic architecture of leaf morphological and physiological traits in a Populus deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ pedigree revealed by quantitative trait locus analysis

Understanding the genetic architecture of leaf morphological and physiological traits will help plant breeders develop high biomass poplar genotypes. Quantitative trait locus (QTL) studies combining next-generation sequencing techniques can advance our understanding of the genetic basis of complex traits. In this study, we measured 13 leaf morphological and physiological traits and identified quantitative trait loci (QTLs) in a Populus deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ F1 population (500 progenies) using a high-density genetic map constructed by whole genome re-sequencing. This linkage map consisted of 5796 single nucleotide polymorphism (SNP) markers assigned to 19 linkage groups (LGs), spanning 2683.80 centimorgans (cM) of genetic length, with an average marker density of 0.46 cM. We identified 109 QTLs on 18 LGs for leaf morphological traits and 55 QTLs on 14 LGs for leaf physiological traits. One-hundred eight putative candidate genes were identified within the candidate genomic region. Co-expression network and gene ontology enrichment analyses suggested that these candidate genes were involved in the photosynthetic process. The differential expression patterns of the CYCLIN (Potri.015G112200) and RED CHLOROPHYLL REDUCTASE (Potri.007G043600) genes between two parents indicated their potential roles in leaf morphological and physiological traits. These findings decipher the genetic architecture of leaf morphological and physiological traits in the P. deltoides ‘Danhong’ × P. simonii ‘Tongliao1’ pedigree and provide candidate genes for future poplar genetic improvement.

59 BASIC BIOLOGICAL SCIENCES↗

A study of mechanistic mapping of novel SNPs to male breast cancer

Alterations in BRCA2, PALB2, CHEK2, and p53 genes have been identified for their association with male breast cancer in various studies. The incidence of male breast cancer in India is consistent with its global rate. The present study was carried out with an aim to evaluate the genetic alterations in male breast cancer patients from Malwa region of Punjab, India. Four male breast cancer patients belonging to different families were recruited from Guru Gobind Singh Medical College and Hospital, Faridkot, India. A total of 51 genes reported with implications in the pathogenesis of breast cancer were screened using next generation sequencing. Germline variations were found in BRCA1, BRCA2, PMS2, p53, and PALB2 genes, previously reported to be associated with MBC as well as FBC. In addition to these, 13 novel missense alterations were detected in eight genes including STK11, FZR1, PALB2, BRCA2, NF2, BAP1, BARD1, and CHEK2. Impact of these missense alterations on structure and function of protein was also analyzed through molecular dynamics simulation. Structural analysis of these single nucleotide polymorphisms (SNPs) revealed significant impact on the encoded protein functioning.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Conversion of Corn Stover Hydrolysates to Acids: Comparison Between Clostridium carboxidivorans P7 and Microbial Communities Developed from Lake Sediment and an Anaerobic Digester

Anaerobic fermentation is an environmentally sustainable technology for converting a variety of feedstocks to biofuels and bioproducts. Considering the complex nature of lignocellulosic hydrolysates, we aimed to investigate product formation from corn stover hydrolysates by using microbial communities under anaerobic conditions. A community developed from lake sediment was able to produce lactic acid from only glucose in the raw or overlimed hydrolysates. Another community from an anaerobic digester, however, was capable of using all hexose and pentose sugars in the raw and undetoxified hydrolysates and released lactic acid at 26.76 g/L. A pure acetogen, Clostridium carboxidivorans P7, was able to grow on the raw and overlimed hydrolysates, too. But the consumption of sugars was minimal and the total released acid concentrations were less than 2 g/L. Next generation sequencing of the enriched community derived from the anaerobic digester revealed the presence of Lactobacillus strains. The predominant species were Lactobacillus parafarraginis (72.6%) and L. buchneri (13.4%). Product titer from using this enriched community can be further enhanced by cultivating at fed-batch or continuous fermentation modes. Results from this study widened the door for producing valuable products from lignocellulosic feedstocks through using mixed cultures.

09 BIOMASS FUELS↗

Knowledge-matching based computational framework for genome-scale metabolic model refinement

Genome-scale metabolic models (GEMs) are mathematically structured knowledge base reconstructed from annotated genome of different organisms. With the advancement of next-generation sequencing technology, many organisms have had their genomes sequenced. However, obtaining a high-quality GEM is highly time-consuming, even with the introduction of several genome-scale reconstruction tools that offer automated draft network generation and gap filling. It has been recognized that the iterative process of manual curation and refinement is the limiting step of GEM development, and how to expedite the GEM refinement is still an open question. As cellular metabolism is a complex system with very high degree of freedom and redundancy, the principles and techniques developed in process systems engineering can be adapted to expedite GEM refinement. In this paper we present a knowledge-matching based computation framework for GEM refinement, and demonstrate the effectiveness of the proposed solution using the refinement of a GEM for Clostridium tyrobutyricum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Virology: The Next Generation from Digital PCR to Single Virion Genomics

In the past 25 years, virology has had major technology breakthroughs stemming first from the introduction of nucleic acid amplification testing, but more recently from the use of next-generation sequencing, digital PCR, and the possibility of single virion genomics. These technologies have and will improve diagnosis and disease state monitoring in clinical settings, aid in environmental monitoring, and reveal the vast genetic potential of viruses. Using the principle of limiting dilution, digital PCR amplifies single molecules of DNA in highly partitioned endpoint reactions and reads each of those reactions as either positive or negative based on the presence or absence of target fluorophore. In this review, digital PCR will be highlighted along with current studies, advantages/disadvantages, and future perspectives with regard to digital PCR, viral load testing, and the possibility of single virion genomics.

59 BASIC BIOLOGICAL SCIENCES↗

A cancer/testis antigen, NY-SAR-35, induces EpCAM, CD44, and CD133, and activates ERK in HEK293 cells

The cancer/testis (CT) antigen NY-SAR-35 gene is located on the X chromosome and is aberrantly expressed in various cancers but not in normal tissues, other than testes. Previously, we reported the expression of NY-SAR-35 enhanced cell growth, proliferation, and invasion in HEK293 and cancer cells. To extend understanding of the NY-SAR-35 gene, we used a next generation sequencing (NGS) approach. NY-SAR-35 expression induced growth, proliferation, metastasis, and stemness genes, as indicated by the up-regulations of CXCR4, EpCAM, CD133, and CD44, at the mRNA and protein levels. The expression of NY-SAR-35 in HEK293 cells significantly increased ERK phosphorylation, but not the phosphorylation of AKT. In HEK293/NY-SAR-35 cells, the expressions of pro-apoptotic proteins, including p53, Bax, and p21, were reduced and that of cyclin E was increased. Also, NY-SAR-35 increased the expressions of pluripotency genes (Nanog, Oct-4, and Sox2) and the ability of HEK293 cells to form colonies. Taken together, the present study indicates NY-SAR-35 functions as a CT antigen that triggers oncogenesis and self-renewal. - Highlights: • To extend our understanding for NY-SAR-35, we performed NGS technology. • Expression of NY-SAR-35 induced EpCAM, CD133, and CD44 at mRNA and protein. • NY-SAR-35 significantly led to increased phosphorylation of ERK and not of that AKT. • NY-SAR-35 increased expression of pluripotency genes and ability of colony formation. • NY-SAR-35 functions as a new CT antigen to trigger oncogenesis and self-renewal.

60 APPLIED LIFE SCIENCES↗

A 2 bp deletion in the mitochondrial ATP 6 gene responsible for the NARP (neuropathy, ataxia, and retinitis pigmentosa) syndrome

Highlights: • A 2 bp deletion of the ATP6 gene causes a truncated a subunit. • The truncated a subunit is responsible for a decrease of complex V activity. • A 2 bp deletion of the ATP6 gene causes a NARP syndrome. Mitochondrial (mt) DNA-associated NARP (neurogenic muscle weakness, ataxia, and retinitis pigmentosa) syndrome is due to mutation in the MT-ATP6 gene. We report the case of a 18-year-old man who presented with deafness, a myoclonic epilepsy, muscle weakness since the age of 10 and further developed a retinitis pigmentosa and ataxia. The whole mtDNA analysis by next-generation sequencing revealed the presence of the 2 bp microdeletion m.9127–9128 del AT in the ATP6 gene at 82% heteroplasmy in muscle and to a lower load in blood (10–20%) and fibroblasts (50%). Using the patient's fibroblasts, we demonstrated a 60% reduction of the oligomycin-sensitive ATPase hydrolytic activity, a 40% decrease in the ATP synthesis and determination of the mitochondrial membrane potential using the fluorescent probe tetramethylrhodamine, ethyl ester indicated a significant reduction in oligomycin sensitivity. In conclusion, we demonstrated that this novel AT deletion in the ATP6 gene is pathogenic and responsible for the NARP syndrome.

60 APPLIED LIFE SCIENCES↗

Distorted antibody repertoire developed in the absence of pre-B cell receptor formation

Highlights: • Leaky B cells in SLC-deficient mice circumvent the pre-BCR checkpoint. • Antibody repertoires differing in VDJ-usage exist in leaky B cells in λ5{sup −}/{sup −} mice. • Leaky B cells do not originate from B1 or particular B2 cells. • The CDR-H3 middle loop in λ5{sup −}/{sup −} bone marrow B cells is enriched in arginines. The pre-B cell receptor (pre-BCR), consisting of the μ heavy chain (μHC) and the surrogate light chain (SLC, Vpre-B and λ5), plays important roles during B cell development. The formation of the pre-BCR, which enables the nascent immunoglobulin HC to associate with the SLC, is considered a prerequisite for B cell development. However, a significant number of peripheral mature (leaky) B cells exist in SLC-deficient mice. These leaky B cells develop in the absence of pre-BCR and do not undergo the pre-BCR checkpoint. The antibody repertoires of leaky B cells thus reflect the absence of pre-BCR function. To investigate how the absence of the pre-BCR is circumvented by these leaky-B cells and examine the effect of the pre-BCR checkpoint on the antibody system, we analyzed the antibody repertoires of λ5-deficient (λ5{sup −/−}) mice using next-generation sequencing. In λ5{sup −/−} mice, spleen B cells displayed different patterns of VDJ-usage, relative to those in wild-type (WT) mice. Moreover, leaky B cells were neither derived from unusual B2 cells, characterized by particular LC gene rearrangements in the absence of pre-BCR signaling, nor from B1 cells, originating from different B cell progenitors. Analysis of the CDR-H3 amino acid sequences of μ-chain repertoires revealed that certain bone marrow B cells with particular CDR-H3 profiles undergo clonal expansion in λ5{sup −/−} mice. Part of these CDR-H3s contain arginine(s) in the middle of the CDR-H3 loop in λ5{sup −/−} mice, whereas few arginine(s) exist in this middle loop in WT CDR-H3s in the absence of clonal expansion. This CDR-H3 feature in λ5{sup −/−} mice presumably reflects the role of the pre-BCR in autoantibody regulation, since arginine(s) are often found in the antigen-binding site of autoantibodies. Here, we present a unique viewpoint on the role of pre-BCR, by assessing the whole antibody repertoire formed in SLC-deficient mice.

60 APPLIED LIFE SCIENCES↗

Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries

With rapid improvements in next-generation sequencing technologies, our knowledge about metabolism of many organisms is rapidly increasing. However, gaps in metabolic networks exist due to incomplete knowledge (e.g., missing reactions, unknown pathways, unannotated and misannotated genes, promiscuous enzymes, and underground metabolic pathways). Here in this review, we discuss recent advances in gap-filling algorithms based on genome-scale metabolic models and the importance of both high-throughput experiments and detailed biochemical characterization, which work in concert with in silico methods, to allow a more accurate and comprehensive understanding of metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial spies and bloggers: programming cells to convert environmental information into discernible signals

Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. Here, in this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.

analyte↗

Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.

59 BASIC BIOLOGICAL SCIENCES↗

A case study of tuning MapReduce for efficient Bioinformatics in the cloud

The combination of the Hadoop MapReduce programming model and cloud computing allows biological scientists to analyze next-generation sequencing (NGS) data in a timely and cost-effective manner. Cloud computing platforms remove the burden of IT facility procurement and management from end users and provide ease of access to Hadoop clusters. However, biological scientists are still expected to choose appropriate Hadoop parameters for running their jobs. More importantly, the available Hadoop tuning guidelines are either obsolete or too general to capture the particular characteristics of bioinformatics applications. In this paper, we aim to minimize the cloud computing cost spent on bioinformatics data analysis by optimizing the extracted significant Hadoop parameters. When using MapReduce-based bioinformatics tools in the cloud, the default settings often lead to resource underutilization and wasteful expenses. We choose k-mer counting, a representative application used in a large number of NGS data analysis tools, as our study case. Experimental results show that, with the fine-tuned parameters, we achieve a total of 4× speedup compared with the original performance (using the default settings). Finally, this paper presents an exemplary case for tuning MapReduce-based bioinformatics applications in the cloud, and documents the key parameters that could lead to significant performance benefits.

97 MATHEMATICS AND COMPUTING↗

Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition

Protists, in particular bacterivores, are essential players in the rhizosphere; thus, how their interactions with bacteria and fungi affect plant productivity and soil nutrient cycles warrants more attention. Using next-generation sequencing of the 18 S rRNA gene, we investigated the distribution of two major protistan phyla, Cercozoa and Endomyxa, across four seasons, and four soil compartments - rhizosphere, root, soil and litter. The sampling was replicated in two forests in Norway and the Czech Republic, in order to test our results across biogeographic scales. Compartment had a major influence in shaping protistan communities, over and above spatial distance and seasonal variation. Protistan diversity was highest in the bulk soil while lowest in the roots, suggesting that the plants select for restricted assemblages of protists. Accordingly, only the root compartment harboured a subset of the bulk soil protistan diversity. In addition, protistan communities showed markedly different distributions according to their feeding modes, with opposite patterns for bacterivores versus omnivores and eukaryvores. The small bacterivorous flagellates (mostly Glissomonadida) were more abundant in roots, while the larger amoeboid eukaryvores (e.g. some of the Cryomonadida and vampyrellids) dominated in soil and in the rhizosphere, and the omnivores (e.g. Euglyphida and part of the Cercomonadida), also large and mostly amoeboid, were more abundant in litter. The current view of the soil microbiome is mostly focused on bacteria and fungi: this detailed study on the community distribution of protists according to their feeding modes reveals the essential role they play in each of the soil compartments, an essential precondition for a detailed understanding of the soil food web and nutrient cycling in forest.

59 BASIC BIOLOGICAL SCIENCES↗

Zinc chloride affects chondrogenesis via VEGF signaling

Highlights: • ZnCl2 increases expression of various chondrogenic signaling intermediates. • VEGF/VEGFR play a key role in modulating levels of chondrogenesis. • Insulin mimetics are an appealing option for improvement of fracture healing. • Axitinib + ZnCl2 treatment results in decreased transcription of chondrogenic genes. Insulin mimetics, including zinc containing compounds, have previously been shown to influence chondrogenesis as it relates to healing of fractures in various preclinical models. However, the mechanism by which these compounds drive chondrogenic differentiation is yet undefined. Here, via next-generation sequencing (NGS) and in vitro functional validation, we show that Zinc Chloride (ZnCl{sub 2}) induces expression of both chondrogenic genes (Sox9, Runx1, collagen) as well as genes associated with VEGF-mediated signal transduction, including VEGF receptors 1 and 2 and their ligands; VEGF-A and VEGF-B. Noticeably, although insulin was able to also induce expression of these pro-angiogenic and pro-chondrogenic genes, the impact of insulin on expression of VEGF receptor and ligand genes was marginal when compared to that of ZnCl{sub 2.} Furthermore, while the VEGFR antagonist, Axitinib, was able to attenuate the pro-chondrogenic effects of both insulin and ZnCl{sub 2}; a reduction in gene and protein expression was most profoundly observed when the antagonist was applied to cells treated with ZnCl{sub 2.} Taken together, these data suggest an important role for the VEGF-mediated signal transduction pathways in the positive effects observed when applying zinc-based compounds as adjuvants for chondrogenesis-mediated fracture healing. In this regard, further mechanistic evaluation of ZnCl{sub 2} and other zinc-containing insulin mimetics may support rational design of therapies targeted for disease indications associated with impaired fracture healing.

60 APPLIED LIFE SCIENCES↗

Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits

The reliable engineering of biological systems requires quantitative mapping of predictable and context-independent expression over a broad range of protein expression levels. However, current techniques for modifying expression levels are cumbersome and are not amenable to high-throughput approaches. Here we present major improvements to current techniques through the design and construction of E. coli genome-wide libraries using synthetic DNA cassettes that can tune expression over a ~10 4 range. The cassettes also contain molecular barcodes that are optimized for next-generation sequencing, enabling rapid and quantitative tracking of alleles that have the highest fitness advantage. We show these libraries can be used to determine which genes and expression levels confer greater fitness to E. coli under different growth conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Synthetic and systems biology for microbial production of commodity chemicals

The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

59 BASIC BIOLOGICAL SCIENCES↗

Base changes in tumour DNA have the power to reveal the causes and evolution of cancer

Next-generation sequencing (NGS) technology has demonstrated that the cancer genomes are peppered with mutations. Although most somatic tumour mutations are unlikely to have any role in the cancer process per se, the spectra of DNA sequence changes in tumour mutation catalogues have the potential to identify the mutagens, and to reveal the mutagenic processes responsible for human cancer. Very recently, a novel approach for data mining of the vast compilations of tumour NGS data succeeded in separating and precisely defining at least 30 distinct patterns of sequence change hidden in mutation databases. At least half of these mutational signatures can be readily assigned to known human carcinogenic exposures or endogenous mechanisms of mutagenesis. A quantum leap in our knowledge of mutagenesis in human cancers has resulted, stimulating a flurry of research activity. We trace here the major findings leading first to the hypothesis that carcinogenic insults leave characteristic imprints on the DNA sequence of tumours, and culminating in empirical evidence from NGS data that well-defined carcinogen mutational signatures are indeed present in tumour genomic DNA from a variety of cancer types. The notion that tumour DNAs can divulge environmental sources of mutation is now a well-accepted fact. This approach to cancer aetiology has also incriminated various endogenous, enzyme-driven processes that increase the somatic mutation load in sporadic cancers. The tasks now confronting the field of molecular epidemiology are to assign mutagenic processes to orphan and newly discovered tumour mutation patterns, and to determine whether avoidable cancer risk factors influence signatures produced by endogenous enzymatic mechanisms. As a result, innovative research with experimental models and exploitation of the geographical heterogeneity in cancer incidence can address these challenges.

59 BASIC BIOLOGICAL SCIENCES↗