Biology Commons^™

Genetic Tool Development In Marine Protists: Emerging Model Organisms For Experimental Cell Biology, Drahomíra Faktorová, R. Ellen R. Nisbet, José A. Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares, Cristina Aresté, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, François Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pía A. Elustondo, Deborah Robertson

Biology

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species …

General Dna Methylation Patterns And Environmentally-Induced Differential Methylation In The Eastern Oyster (Crassostrea Virginica), Yaamini R. Venkataraman, Alan M. Downey-Wall, Justin Ries, Isaac Westfield, Samuel J. White, Steven B. Roberts, Kathleen E. Lotterhos

Biology

Epigenetic modification, specifically DNA methylation, is one possible mechanism for intergenerational plasticity. Before inheritance of methylation patterns can be characterized, we need a better understanding of how environmental change modifies the parental epigenome. To examine the influence of experimental ocean acidification on eastern oyster (Crassostrea virginica) gonad tissue, oysters were cultured in the laboratory under control (491 ± 49 μatm) or high (2550 ± 211 μatm) pCO2 conditions for 4 weeks. DNA from reproductive tissue was isolated from five oysters per treatment, then subjected to bisulfite treatment and DNA sequencing. Irrespective of treatment, DNA methylation was primarily found in gene …

Mentzelia Pectinata Var. Chrysopetala (Loasaceae), A Yellow-Petaled Race From West-Central California, David J. Keil, Joshua M. Brokaw

Biology

Mentzelia pectinata Kellogg var. chrysopetala Keil & Brokaw, var. nov., is a yellow-petaled race of the otherwise orange-petaled M. pectinata, a species endemic to central California. The yellow-and orange-petaled varieties are largely allopatric, with var. chrysopetala nearly restricted to San Luis Obispo County, whereas var. pectinata extends eastward into the dry hills and mountains around the southern end of the San Joaquin Valley, including eastern portions of San Luis Obispo County. Petals of var. chrysopetala are golden yellow, usually with orange bases, unlike the petals of var. pectinata, which are coppery orange with red-orange bases. We designate a neotype for …

Unexpected Predicted Length Variation For The Coding Sequence Of The Sleep Related Gene, Bhlhe41 In Gorilla Amidst Strong Purifying Selection Across Mammals, Krishna Unadkat, Justen B. Whittall

Biology

There is a molecular basis for many sleep patterns and disorders involving circadian clock genes. In humans, “short-sleeper” behavior has been linked to specific amino acid substitutions in BHLHE41 (DEC2), yet little is known about variation at these sites and across this gene in mammals. We compare BHLHE41 coding sequences for 27 mammals. Approximately half of the coding sequence was invariable at the nucleotide level and close to three-quarters of the amino acid alignment was identical. No other mammals had the same “short-sleeper” amino acid substitutions previously described from humans. Phylogenetic analyses based on the nucleotides of the coding sequence …

Unraveling The Role Of The Enigmatic Matk Maturase In Chloroplast Group Iia Intron Excision, Michelle M. Barthet, Christopher L. Pierpont, Emilie Katherine Tavernier

Biology

Maturases are prokaryotic enzymes that aid self-excision of introns in precursor RNAs and have evolutionary ties to the nuclear spliceosome. Both the mitochondria and chloroplast, due to their prokaryotic origin, encode a single intron maturase, MatR for the mitochondria and MatK for the chloroplast. MatK is proposed to aid excision of seven different chloroplast group IIA introns that reside within precursor RNAs for essential elements of chloroplast function. We have developed an in vitro activity assay to test chloroplast group IIA intron excision. Using this assay, we demonstrate self-excision of the group IIA intron of the second intron of rps12 …

Identifying Viruses From Metagenomic Data Using Deep Learning, Jie Ren, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin, Fengzhu Sun

Biology

Background: The recent development of metagenomic sequencing makes it possible to massively sequence microbial genomes including viral genomes without the need for laboratory culture. Existing reference-based and gene homology-based methods are not efficient in identifying unknown viruses or short viral sequences from metagenomic data. Methods: Here we developed a reference-free and alignment-free machine learning method, DeepVirFinder, for identifying viral sequences in metagenomic data using deep learning. Results: Trained based on sequences from viral RefSeq discovered before May 2015, and evaluated on those discovered after that date, DeepVirFinder outperformed the state-of-the-art method VirFinder at all contig lengths, achieving AUROC 0.93, 0.95, …

Influence Of Ocean Acidification On Eastern (Crassostrea Virginica) And Pacific Oyster (Crassostrea Gigas) Dna Methylation, Yaamini R. Venkataraman, Alan M. Downey-Wall, Kathleen E. Lotterhos, Steven B. Roberts

Biology

Epigenetic modification, specifically DNA methylation, is one possible mechanism for transgenerational plasticity. Before inheritance of methylation patterns can be characterized we need a better understanding of how environmental change modifies the parental epigenome. The influence of experimental ocean acidification on DNA methylation was examined in gonad tissue two congeneric species: eastern (Crassostrea virginica) and Pacific oysters (Crassostrea gigas). Methylation islands were characterized in both species, and were found primarily in gene bodies. There were no conserved genes in methylation islands between species. Differentially methylated loci (DML) were found in gene bodies, with 598 in C. virginica and 628 in C. …

Proteasome Inhibition Rapidly Exacerbates Photoinhibition And Impedes Recovery During High Light Stress In Chlamydomonas Reinhardtii, Felipe Mendoza, Carson Berry, Laura Prestigiacomo, Doug Van Hoewyk

Biology

Background: Proteasomes remove regulatory proteins in eukaryotic cells, and control a variety of plant processes. Proteasomes are localized to the cytosol and nuclear, but their role in plant biology has recently been extended to chloroplasts, where it regulates TOC complex. This is turn controls the import of nuclear-encoded chloroplastic proteins, which remodels the chloroplast proteome and facilitates proper developmental transitions. Proteasomal regulation of the TOC complex also alleviates stressors that generate reactive oxygen species. These recent advances motivated us to determine if proteasome inhibition rapidly alters photosynthetic processes stemming from photoinhibition induced by high light. Results: The short-term effects of …

A Mafg-Lncrna Axis Links Systemic Nutrient Abundance To Hepatic Glucose Metabolism, Jenny Link, Martha Pradas-Juni, Nils R. Hansmeier, Elena Schmidt, Bjørk Ditlev Larsen, Paul Klemm, Nicola Meola, Hande Topel, Rute Loureiro, Ines Dhaouadi, Christoph A. Kiefer, Robin Schwarzer, Sajjad Khani, Matteo Oliverio, Motoharu Awazawa, Peter Frommolt, Joerg Heeren, Ludger Scheja, Markus Heine, Christoph Dieterich, Hildegard Büning, Ling Yang, Haiming Cao, Dario F. De Jesus, Rohit Kulkarni, Branko Zevnik, Simon E. Tröder, Uwe Knippschild, Peter A. Edwards, Richard G. Lee, Masayuki Yamamoto, Igor Ulitsky, Eduardo Fernandez-Rebollo, Thomas Q. De Aguiar Vallim, Jan-Wilhelm Kornfeld

Biology

Obesity and type 2 diabetes mellitus are global emergencies and long noncoding RNAs (lncRNAs) are regulatory transcripts with elusive functions in metabolism. Here we show that a high fraction of lncRNAs, but not protein-coding mRNAs, are repressed during diet-induced obesity (DIO) and refeeding, whilst nutrient deprivation induced lncRNAs in mouse liver. Similarly, lncRNAs are lost in diabetic humans. LncRNA promoter analyses, global cistrome and gain-of-function analyses confirm that increased MAFG signaling during DIO curbs lncRNA expression. Silencing Mafg in mouse hepatocytes and obese mice elicits a fasting-like gene expression profile, improves glucose metabolism, de-represses lncRNAs and impairs mammalian target of …

X Chromosome Dosage Of Histone Demethylase Kdm5c Determines Sex Differences In Adiposity, Jenny C. Link, Carrie B. Wiese, Xuqi Chen, Rozeta Avetisyan, Emilio Ronquillo, Feiyang Ma, Xiuqing Guo, Jie Yao, Matthew Allison, Yii-Der Ida Chen, Jeremy I. Rotter

Biology

Males and females differ in body composition and fat distribution. Using a mouse model that segregates gonadal sex (ovaries and testes) from chromosomal sex (XX and XY), we showed that XX chromosome complement in combination with a high-fat diet led to enhanced weight gain in the presence of male or female gonads. We identified the genomic dosage of Kdm5c, an X chromosome gene that escapes X chromosome inactivation, as a determinant of the X chromosome effect on adiposity. Modulating Kdm5c gene dosage in XX female mice to levels that are normally present in males resulted in reduced body weight, fat …

Biogeography Of American Northwest Hot Spring A/B′-Lineage Synechococcus Populations, Eric D. Becraft, Jason M. Wood, Frederick M. Cohan, David M. Ward

Biology

Previous analyses have shown how diversity among unicellular cyanobacteria inhabiting island-like hot springs is structured relative to physical separation and physiochemical differences among springs, especially at local to regional scales. However, these studies have been limited by the low resolution provided by the molecular markers surveyed. We analyzed large datasets obtained by high-throughput sequencing of a segment of the photosynthesis gene psaA from samples collected in hot springs from geothermal basins in Yellowstone National Park, Montana, and Oregon, all known from previous studies to contain populations of A/B′-lineage Synechococcus. The fraction of identical sequences was greater among springs separated by …

Hiding In Plain Sight: The Globally Distributed Bacterial Candidate Phylum Pauc34f, Michael L. Chen, Eric D. Becraft, Maria Pachladaki, Julia M. Brown, Jessica K. Jarett, Josep M. Gasol, Nikolai V. Ravin, Duane P. Moser, Takuro Nunoura, Gerhard J. Herndl, Tanja Woyke, Ramunas Stepanauskas

Biology

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while …

Whole Plastome Sequencing Within Silene Section Psammophilae Reveals Mainland Hybridization And Divergence With The Balearic Island Populations, José Carlos Del Valle, Inés Casimiro-Soriguer, Mᵃ Luisa Buide, Eduardo Narbona, Justen B. Whittall

Biology

Reconstructing the phylogenetic relationships within Caryophyllaceae tribe Sileneae has been obscured by hybridization and incomplete lineage sorting. Silene is the largest genus in the Caryophyllaceae, and unraveling its evolutionary history has been particularly challenging. In order to infer the phylogenetic relationships among the five species in Silene section Psammophilae, we have performed a genome skimming approach to acquire the complete plastid genome (cpDNA), nuclear ribosomal cistron (nrDNA), and partial mitochondrial genome (mtDNA). We have included 26 populations, representing the range of each species' distribution. This section includes five morphologically similar species endemic to the Iberian Peninsula and Balearic Islands …

Stability Of Petal Color Polymorphism: The Significance Of Anthocyanin Accumulation In Photosynthetic Tissues, José Carlos Del Valle, Cristina Alcalde-Eon, Mª Teresa Escribano-Bailón, Mª Luisa Buide, Justen B. Whittall, Eduardo Narbona

Biology

Background: Anthocyanins are the primary source of colour in flowers and also accumulate in vegetative tissues, where they have multiple protective roles traditionally attributed to early compounds of the metabolic pathway (flavonols, flavones, etc.). Petal-specific loss of anthocyanins in petals allows plants to escape from the negative pleiotropic effects of flavonoid and anthocyanins loss in vegetative organs, where they perform a plethora of essential functions. Herein, we investigate the degree of pleiotropy at the biochemical scale in a pink-white flower colour polymorphism in the shore campion, Silene littorea. We report the frequencies of pink and white individuals across 21 populations …

Tissue-Specific 3 Prime-End Adenylation Of Mir-125b Mediates Cell Survival, Matthew T. Blahna, Jean-Charles Neel, Ge Yu, Justin Louie, Prajakta Ghatpande, Giorgio Lagna, Akiko Hata

Biology

Next-generation sequencing has uncovered microRNAs (miRNAs) that undergo sequence modifications, known as isomiRs. Their physiological significance, however, remains uncertain, partly because they generally comprise a small fraction of total miRNAs. Here we report that more than 60% of miR-125b, one of the most abundant miRNAs in vascular smooth muscle cells (vSMC), exists as an edited isoform containing a non-templated adenosine residue at the 3 prime-end (miR-125b+A). The properties of miR-125b+A, such as stability and subcellular localization, are similar to those of canonical miR-125b, but miR-125b+A more potently inhibits the expression of a subgroup of targets, including the apoptosis effector Caspase-6 …

Rapid And Efficient Purification Of Drosophila Homeodomain Transcription Factors For Biophysical Characterization, Rachel Orlomoski, Aaron Bogle, Jeanmarie Loss, Rylee Simons, Jacqueline M. Dresch, Robert A. Drewell, Donald E. Spratt

Biology

Homeodomain transcription factors (HD TFs) are a large class of evolutionarily conserved DNA binding proteins that contain a basic 60-amino acid region required for binding to specific DNA sites. In Drosophila melanogaster, many of these HD TFs are expressed in the early embryo and control transcription of target genes in development through their interaction with cis-regulatory modules. Previous studies where some of the Drosophila HD TFs were purified required the use of strong denaturants (i.e. 6 M urea) and multiple chromatography columns, making the downstream biochemical examination of the isolated protein difficult. To circumvent these obstacles, we have developed a …

Megaphylogeny Resolves Global Patterns Of Mushroom Evolution, Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis Desjardin, Péter Finy, József Geml, Sajeet Haridas, Karen Hughes, Alfredo Justo, Dariusz Karasiński, Ivona Kautmanova, Brigitta Kiss, Sándor Kocsubé, David Hibbett

Biology

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with …

Where Has All The Ceanothus Megacarpu S Gone?, Alden Kruse, Hudson Kruse, Naomi Kruse

Biology

Background: Wildfire is a large part of the chaparral biome, where seedlings from sclerophyllous plants need fire to crack the seed coat. When shrubs reach maturity they produce seeds, allowing for greater genetic diversity and variation. We visually, noticed that the coastal chaparral appeared to be in distress and suspected climate extremes of drought and frequent fire were the cause.

Method: Following the Woolsey Fire (2018) we quadrat sampled three chaparral sites on the Pepperdine Campus in Malibu, CA. All three experienced fire and drought. One site had been subjected to five fires in less than 35 years. Another experienced …

Les Chitinases, Témoins De La Radiation Des Mammifères Placentaires / Chitinase Genes Provide Insights Into The Radiation Of Placental Mammals, Christopher A. Emerling, Frédéric Delsuc, Michael W. Nachman

Biology

No abstract provided.

Quantimus: A Machine Learning-Based Approach For High Precision Analysis Of Skeletal Muscle Morphology, Sylvia A. Vetrone, Jenna M. Kastenschmidt, Kyle L. Ellefsen, Ali H. Mannaa, Jesse J. Giebel, Rayan Yahia, Rachel E. Ayer, Phillip Pham, Rodolfo Rios, Tahseen Mozaffar, S. Armando Villalta

Biology

Skeletal muscle injury provokes a regenerative response, characterized by the de novo generation of myofibers that are distinguished by central nucleation and re-expression of developmentally restricted genes. In addition to these characteristics, myofiber crosssectional area (CSA) is widely used to evaluate muscle hypertrophic and regenerative responses. Here, we introduce QuantiMus, a free software program that uses machine learning algorithms to quantify muscle morphology and molecular features with high precision and quick processing-time. The ability of QuantiMus to define and measure myofibers was compared to manual measurement or other automated software programs. QuantiMus rapidly and accurately defined total myofibers and measured …

Evolution And Diversification Of Fruitfull Genes In Solanaceae, Christopher A. Emerling, Dinusha C. Maheepala, Alex Rajewski, Jenna Macon, Maya Strahl, Natalia Pabón-Mora, Amy Litt

Biology

Ecologically and economically important fleshy edible fruits have evolved from dry fruit numerous times during angiosperm diversification. However, the molecular mechanisms that underlie these shifts are unknown. In the Solanaceae there has been a major shift to fleshy fruits in the subfamily Solanoideae. Evidence suggests that an ortholog of FRUITFULL (FUL), a transcription factor that regulates cell proliferation and limits the dehiscence zone in the silique of Arabidopsis, plays a similar role in dry-fruited Solanaceae. However, studies have shown that FUL orthologs have taken on new functions in fleshy fruit development, including regulating elements of tomato ripening …

Odontogenic Ameloblast-Associated (Odam) Is Inactivated In Toothless/ Enamelless Placental Mammals And Toothed Whales, Christopher A. Emerling, Mark S. Springer, John Gatesy, Jason Randall, Matthew A. Collin, Nikolai Hecker, Michael Hiller, Frédéric Delsuc

Biology

The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we leverage the power of natural selection to test competing hypotheses that ODAM is tooth-specific versus pleiotropic. Specifically, we compiled and screened complete protein-coding sequences, plus sequences for flanking intronic regions, for ODAM in 165 placental mammals to determine if this gene contains inactivating mutations in lineages that either lack teeth (baleen whales, pangolins, anteaters) …

Four Draft Single-Cell Genome Sequences Of Novel, Nearly Identical Kiritimatiellaeota Strains Isolated From The Continental Deep Subsurface, Joshua D. Sackett, Brittany R. Kruger, Eric Becraft, Jessica K. Jarett, Ramunas Stepanauskas, Tanja Woyke, Duane P. Moser

Biology

The recently proposed bacterial phylum Kiritimatiellaeota represents a globally distributed monophyletic clade distinct from other members of the Planctomycetes, Verrucomicrobia, and Chlamydiae (PVC) superphylum. Here, we present four phylogenetically distinct single-cell genome sequences from within the Kiritimatiellaeota lineage sampled from deep continental subsurface aquifer fluids of the Death Valley Regional Flow System in the United States.

Hydrogen-Based Metabolism As An Ancestral Trait In Lineages Sibling To The Cyanobacteria, Paula B. Matheus Camevali, Frederik Schulz, Cindy J. Castelle, Rose S. Kantor, Patrick M. Shih, Itai Sharon, Joanne M. Santini, Matthew R. Olm, Yuki Amano, Brian C. Thomas, Karthik Anantharaman, David Burstein, Eric D. Becraft, Ramunas Stepanauskas, Tanja Woyke, Jillian F. Banfield

Biology

The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria and Sericytochromatia, may constrain the metabolic platform in which aerobic respiration arose. Here, we analyze genomic sequences and predict that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents. The genomes of ocean-associated Margulisbacteria encode an electron transport chain that may support aerobic growth. Some Saganbacteria genomes encode various hydrogenases, and others may be able to use …

Characterization Of Pacific Oyster Crassostrea Gigas Proteomic Response To Natural Environmental Differences, Yaamini R. Venkataraman, Emma Timmins-Schiffman, Micah J. Horwith, Alexander T. Lowe, Brook Nunn, Brent Vadopalas, Laura H. Spencer, Steven B. Roberts

Biology

Global climate change is rapidly altering coastal marine ecosystems that are important for food production. A comprehensive understanding of how organisms will respond to these complex environmental changes can come only from observing and studying species within their natural environment. To this end, the effects of environmental drivers—pH, dissolved oxygen content, salinity, and temperature—on Pacific oyster Crassostrea gigas physiology were evaluated in an outplant experiment. Sibling juvenile oysters were outplanted to eelgrass and unvegetated habitat at 5 different estuarine sites within the Acidification Nearshore Monitoring Network in Washington State, USA, to evaluate how regional environmental drivers influence molecular physiology. Within …

Microbial Community In Hyperalkaline Steel Slag-Fill Emulates Serpentinizing Springs, J Ingemar Ohlsson, Jay T. Osvatic, Eric D. Becraft, Wesley D. Swingley

Biology

To date, a majority of studies of microbial life in hyperalkaline settings focus on environments that are also highly saline (haloalkaline). Haloalkaline conditions oer microbes abundant workarounds to maintain pH homeostasis, as salt ions can be exchanged for protons by dedicated antiporter proteins. Yet hyperalkaline freshwater systems also occur both naturally and anthropogenically, such as the slag fill aquifers around former Lake Calumet (Chicago, IL, USA). In this study, 16S rRNA gene sequences and metagenomic sequence libraries were collected to assess the taxonomic composition and functional potential of microbes present in these slag-polluted waterways. Relative 16S rRNA gene abundances in …

Optimizing De Novo Genome Assembly From Pcr-Amplified Metagenomes, Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent R. Northen, Matthew B. Sullivan, Virginia I. Rich, Rex R. Malmstrom, Emiley A. Eloe-Fadrosh

Biology

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified …

Nuclear Envelope Organization In Dictyostelium Discoideum, Petros Batsios, Ralph Gräf, Michael P. Koonce, Denis A. Larochelle, Irene Meyer

Biology

The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export. The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun1, as well as with the LEM/HeH-family protein Src1. Sun1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun1 usually forms a so-called LINC complex. Two proteins with functions reminiscent of …

Dynamics Of Prochlorococcus Diversity And Photoacclimation During Short-Term Shifts In Water Column Stratification At Station Aloha, Anne W. Thompson, Ger Van Den Engh, Nathan A. Ahlgren, Kathleen Kouba, Samantha Ward, Samuel T. Wilson, David M. Karl

Biology

The cyanobacterium Prochlorococcus is the dominant phototroph in surface waters of the vast oligotrophic oceans, the foundation of marine food webs, and an important component of global biogeochemical cycles. The prominence of Prochlorococcus across the environmental gradients of the open ocean is attributed to its extensive genetic diversity and flexible chlorophyll physiology, enabling light capture over a wide range of intensities. What remains unknown is the balance between temporal dynamics of genetic diversity and chlorophyll physiology in the ability of Prochlorococcus to respond to a variety of short (approximately 1 day) and longer (months to year) changes in the environment. …

Phylogenetic Taxon Definitions For Fungi, Dikarya, Ascomycota And Basidiomycota, David S. Hibbett, Meredith Blackwell, Timothy Y. James, Joseph W. Spatafora, John W. Taylor, Rytas Vilgalys

Biology

Phylogenetic taxon definitions (PTDs) are explicit, phylogeny-based statements that specify clades. PTDs are central to the system of rank-free classification that is governed by the PhyloCode, but they can also be used to clarify the meanings of ranked names. We present PTDs for four major groups: Fungi, Dikarya, Ascomycota, and Basidiomycota.