Category Archives: Science – Career – Publishing

January 12, 2015

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Microbiome of pregnancy and birth

Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome – Amanda L. Thompson – Frontiers in Cellular and Infection Microbiology

Human oral microbiome

Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population – Z Qi – International Endodontic Journal

Human gut microbiome
Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation – Mei San Tang – Gut Microbes

Intestinal microbiota in metabolic diseases: From bacterial community structure and functions to species of pathophysiological relevance – Thomas Clavel – Gut Microbes

Editorial: a simple faecal preparation protocol for faecal microbiota transplantation – C. R. Kelly – Alimentary Pharmacology & Therapeutics

Human skin microbiome

Microbiology of diabetic foot infections: from Louis Pasteur to ‘crime scene investigation’ – Anne Spichler – BMC Medicine

Human urinary tract microbiome

The human urine virome in association with urinary tract infections – Tasha M. Santiago-Rodriguez – Frontiers in Microbiology

Animal microbiome

Normal bacterial conjunctival flora in the Huacaya alpaca (Vicugna pacos) – Goedele Storms – Veterinary Ophthalmology

Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla) – Miguel Carda Diéguez – Frontiers in Microbiology

Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome – Inna Rozman Grinberg – FEMS Microbiology Letters

Master Thesis: Predominant fecal microbiota of captive adult cheetahs housed in European zoos: a cross-sectional study – Niloufar Majdzadeh – Ghent University

Plant microbiome

Plant–microbe interactions: Microbiome remote control – Christopher Surridge – Nature Plants

Impact of plant development on the rhizobacterial population of Arachis hypogaea: a multifactorial analysis – Shyamalina Haldar and Sanghamitra Sengupta

Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube – Peng Liu – BioMed Research International

Soil, sediment, sludge microbiome

Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India – Gagandeep Kaur – 3 Biotech

Nitrogen and methanogen community composition within and among three Sphagnum dominated peatlands in Scandinavia – Magalí Martí – Soil Biology and Biochemistry

Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers – Feng Guo – Nature Scientific Reports

Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra – Tatiana A. Semenova – Molecular Ecology

Microbial community composition of transiently wetted Antarctic Dry Valley soils – Thomas D. Neiderberger – Frontiers in Microbiology

Water microbiome

Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity – Gourvendu Saxena – Environmental Science & Technology

An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics – Shangjin Tan – Journal of Phycology

Phages and viruses

(also see above) The human urine virome in association with urinary tract infections – Tasha M. Santiago-Rodriguez – Frontiers in Microbiology

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells – Liana Fasching – Cell Reports

Probiotics

Systematic discovery of probiotics – Samuel C Forster & Trevor D Lawley – Nature Biotechnology

Microbes in the News

Prebiotics: Yeast Is Healthy, And So Are Bacteria That Help Us Break Down Bread And Beer – Science 2.0

Stop Killing the Good Guys! Protect Your Child’s Microbiome From Antibiotic Overuse – Aviva Romm – Huffington Post

Mounting research tightens gut microbial connection with the brain – MedicalXpress
http://medicalxpress.com/news/2015-01-mounting-tightens-gut-microbial-brain.html

Intestinal bacteria study uses Zingerman’s bread – Lea Giotto – The Michigan Daily

Are We Ruled by Our Microbiome? – Qiagen

Could Gut Microbes Help Us Treat Brain Disorders? – Kavli Foundation – Labmanager

Bacteria could contribute to development of wound-induced skin cancer – EurekAlert

Revenge of the bacteria? Earth Talk – August FreePress

Do viruses make us smarter? – Science Daily

The Doctor Who Championed Hand-Washing And Briefly Saved Lives – Rebecca Davis – NPR Morning Edition

Love your gut – and help your body shift those festive pounds – Kathie Swift – Daily Mail

Science, publishing, career

Life sciences workforce trends evolve with the industry – Kathy L Nugent & Lori Lindburg – Nature Biotechnology

12 Common Mistakes In Empirical Social Science – Fred Phillips – Science 2.0

How The War On Science Affects Us All – Greg Satell – Forbes

Bik’s Picks

Devil is in the detail: Evolution of color in plants and animals – Science Daily’

This cannot be statistically sound: Number Of Large Earthquakes Dropped 60 Percent In 2014 – Science 2.0

Why OCD Is ‘Miserable’: A Science Reporter’s Obsession With Contracting HIV – Shots/Fresh Air – NPR

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January 8, 2015

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Human gut microbiome

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation – T. W. Cullen – Science

Review: Ancient human microbiomes – Christina Warinner – Journal of Human Evolution

Microbiota-Mediated Inflammation and Antimicrobial Defense in the Intestine – Silvia Caballero and Eric G. Pamer – Annual Review of Immunology

Animal models of microbiome research

Opposite effects of anthelmintic treatment on microbial infection at individual versus population scales – Vanessa O. Ezenwa, Anna E. Jolles – Science

Plant microbiome

Engineering the plant rhizosphere – Yanxia Zhang – Current Opinion in Biotechnology

Soil and sediment microbiome

Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment (Kartchner Caverns, AZ, USA) (video) – Lin Zhang – JOVE

Sedimentology and Sequence Stratigraphy of the Late Precambrian Carbonates of the Mbuji-Mayi Supergroup in the Sankuru-Mbuji-Mayi-Lomami-Lovoy Basin (Democratic Republic of the Congo) – Franck Delpomdor – Geology and Resource Potential of the Congo Basin

Soil biology for resilient, healthy soil – R. Michael Lehman – Journal of Soil and Water Conservation

Techniques

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform – Yoon-Seong Jeon – Journal of Microbiology

Microbes in the news

Gut bacteria, prebiotics and the link between helping stress, anxiety and depression – Clio Corn – Independent

What’s lurking in your microbiome? Possibly, a cure for disease – Jon Gertner – FastCompany

Could gut bacteria that help us digest beer and bread fight disease, too? – Phys.org

Delivery Mode Alters Newborn’s First Bacterial Exposure How microbiome develops after birth could affect later-life immunity – Bridget M. Kuehn – Gastroenterology and Endoscopy News

CAMI Hosts Community Challenge for Assessing Metagenomes – Joint Genome Institute

Consumer-Funded Test Finds 11 of 12 Pet Foods Contaminated – James Andrews – Food Safety News

Science, publishing, career

My metamorphosis – Elizabeth A. Marchio – Science

A multi-journal partnership to highlight joint first-authors of manuscripts – M Bishr Omary – Gut

Introductory Comments for the Scientific Ethics Theme – Beth A. Fischer – ASM Journal of Microbiology and Biology Education

Exaggerated science reporting – who’s to blame? – NewsWorks

Bik’s Picks

Monkeys can learn to see themselves in the mirror – Science Daily

Poker program Cepheus is unbeatable, claim scientists – The Guardian

Super-insulated clothing could eliminate need for indoor heating – Lisa Zyga – Phys.org

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January 6, 2015

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Human gut microbiome

The involvement of gut microbiota in inflammatory bowel disease pathogenesis: potential for therapy – Giovanni Cammarota – Pharmacology & Therapeutics

Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches – Montserrat Dueñas – Antioxidants

Human respiratory microbiome

Cost-effective pooling of DNA from nasopharyngeal swab samples for large-scale detection of bacteria by real-time PCR – Sophie Edouard – Journal of Clinical Microbiology

Animal models of microbiome research

Effects of dietary mono- and multiprobiotic strains on growth performance, gut bacteria and body composition of Javanese carp (Puntius gonionotus, Bleeker 1850) – S.K. Allameh – Aquaculture Nutrition

Animal microbiome

Harlequin ladybird: Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics – Débora P. Paula – Molecular Ecology Resources

Protist microbiome

Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera) – Masashi Tsuchiya – The Journal of Eukaryotic Microbiology

Plant microbiome

Synergists and antagonists in the rhizosphere modulate microbial communities and growth of Quercus robur L. – Fuensanta Caravaca – Soil Biology and Biochemistry

Soil microbiome

Examination of biotic and abiotic controls of soil bacterial diversity under perennial shrubs in xeric soils – Naama Berg – CATENA

Two Metagenomes from Late Pleistocene Northeast Siberian Permafrost – Kirill Krivushin – Genome Announcements

Extractable N and microbial community structure respond to grassland restoration regardless of historical context and soil composition – Sara Jo M. Dickens – AoB Plants

Methane dynamics in an alpine fen: A field based study on methanogenic and methanotrophic microbial communities – Alessandro G. Franchini – FEMS Microbiology Ecology

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients – Hamed Azarbad – FEMS Microbial Ecology

Effect of biostimulation, temperature and salinity on respiration activities and bacterial community composition in an oil polluted desert soil – Raeid M.M. Abed – International Biodeterioration & Biodegradation

High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community – Masayuki Ushio – Soil Biology and Biochemistry

Water microbiome

Oil-derived marine aggregates – hot spots of polysaccharide degradation by specialized bacterial communities – Carol Arnosti – Deep Sea Research Part II: Topical Studies in Oceanography

Bioreactor and wastewater microbiomes

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors – Yu Xia – Applied Microbiology and Biotechnology

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw – Christopher W Simmons – Biotechnology for Biofuels

Techniques

Protocols for Metagenomic Library Generation and Analysis in Petroleum Hydrocarbon Microbe Systems – Stephanie M. Moormann – Springer Protocols Handbooks 2014

Science, publishing and career

Assessing Research Productivity: A new way of evaluating academics’ research output using easily obtained data – Ushma S. Neill – The Scientist

How many scientific papers are not original? – Michael Lesk – PNAS USA

Know Your PIO: Scientists and public information officers share several common goals. Here’s how to collaborate effectively – Tracy Vence – The Scientist

Microbes in the news

Signs of mother’s diet, birth delivery mode in human milk microbiome – EA Quinn – Genetic Literacy Project

Celebrate your fat – it’s fighting off infection – Clare Wilson – New Scientist

Common cold really is triggered by chilly weather, Yale scientists find – Sarah Knapton – The Telegraph

Picturing Infection: whole-animal, light-based imaging of infected small mammals – Kelly Rae Chi – The Scientist

Bik’s Picks

New evidence on the origin of carnivorous plants – Thomas J. Givnish – PNAS USA

Inching toward the 3D genome – Elizabeth Pennisi – Science

Chopsticks or spoon: The impact of eating methods on eating rate and glycemic response in healthy adults – Lijuan Sun – Physiology & Behavior

Anti-Vaxxers Are Idolizing the Amish, Inexplicably – Olga Khazan – The Atlantic

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December 28, 2014

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Human oral microbiome

Periodontitis: from microbial immune subversion to systemic inflammation – George Hajishengallis – Nature Reviews Immunology

Microbiology of Oral Biofilm-Dependent Diseases: Have We Made Significant Progress to Understand and Treat These Diseases? – Ana Paula Vieira Colombo – Current Oral Health Reports

Human skin microbiome

Dynamics of the surgical microbiota along the cardiothoracic surgery pathway – Sara Romano-Bertrand – Frontiers in Microbiology

Human gut microbiome

Decreased Bacterial Diversity Characterizes the Altered Gut Microbiota in Patients With Psoriatic Arthritis, Resembling Dysbiosis in Inflammatory Bowel Disease – Jose U. Scher – Arthritis & Rheumatology

Insights Into the Role of the Microbiome in Obesity and Type 2 Diabetes – Annick V. Hartstra – Diabetes Care

* The gut microbiota and its role in the development of allergic disease: a wider perspective – C. E. West – Clinical & Experimental Allergy

The power in numbers: Gut microbiota in Parkinson’s disease – Joaquin A. Vizcarra – Movement Disorders

Childhood Obesity: A Role for Gut Microbiota? – Marina Sanchez – Int. J. Environ. Res. Public Health

Animal models of microbiome

Impact of the gut microbiota on rodent models of human disease – Axel Kornerup Hansen – World Journal of Gastroenterology

Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract – Mark J. Koenigsknecht – Infection and Immunity

Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease – Yasushi Minamoto – Gut Microbes

Intermittent hypoxia alters gut microbiota diversity in a mouse model of sleep apnoea
Isabel Moreno-Indias – European Respiratory Journal

Bioreactor models

Lead toxicity to the performance, viability, and community composition of activated sludge microorganisms – Husen Zhang – Environmental Science & Technology

Animal microbiome

Diet strongly influences the gut microbiota of surgeonfishes – Sou Miyake – Molecular Ecology

Plant microbiome

21st century agriculture: integration of plant microbiomes for improved crop production and food security – Angela Sessitsch and Birgit Mitter – Microbial Biotechnology

Soil microbiome

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield – Thomas Rime – Molecular Ecology

Changes in the composition and diversity of bacterial communities 13 years after soil reclamation of abandoned mine land in eastern China – Yuanyuan Li – Ecological Research

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station – Deborah A. Repert – Journal of Geophysical Research: Biogeosciences

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation – Annelie Steinbach – ISME Journal

Different vegetable crop rotations affect soil microbial communities and soilborne diseases of potato and onion: literature review and a long-term field evaluation – PJ Wright – New Zealand Journal of Crop and Horticultural Science

Water microbiome

* Biogeography and ecology of the rare and abundant microbial lineages in deep-sea – Rika E. Anderson – FEMS Microbiology Ecology

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage – Lin-xing Chen – ISME Journal

Microbes of the built environment

Indoor bioaerosol dynamics – William W Nazaroff – Indoor Air

Bioinformatics

An improved method to set significance thresholds for β diversity testing in microbial community comparisons – Arda Gülay and Barth F. Smets – Environmental Microbiology

Metabolomics

Reevaluating the hype: Four bacterial metabolites under scrutiny – Esther Eleonore Fröhlich – European Journal of Microbiology and Immunology

Microbes in the news

Discovering microbiology – Nicholas P Money – Oxford University Press

The Microbes in Your Kitchen (Or in your Starbucks mocha) – Kevin Bonham – Scientific American

Science, Publishing, Career

Science is the most ‘future proof’ degree: Engineering and chemistry seen as courses likely to lead to an adaptable career – Laura Clark – Daily Mail

Bik’s Picks

Dr. Oz gets roasted in science journal’s Christmas edition — science roundup extra (video, links) – Susannah L. Bodman – Oregon Live

Science Explains Why The Best BBQ Is Slow Cooked – Patrick Allan – LifeHacker

The Shapes of Snowflakes – CompoundChem

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December 23, 2014

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Microbiome publications are definitely not taking a winter break, so here is your holiday update. Merry Christmas to those who celebrate!

Human oral microbiome

Serum IgG Antibody Levels to Periodontal Microbiota Are Associated with Incident Alzheimer Disease – James M. Noble – PLOS ONE

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle – Xuesong He – PNAS USA

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant
and periodontal sites – Simone Schaumann – BMC Oral Health

Human respiratory microbiome

The Microbial Community of the Cystic Fibrosis Airway Is Disrupted in Early Life – Julie Renwick – PLOS ONE

Human gut or general microbiome
Effects of bowel cleansing on the intestinal microbiota – Jonna Jalanka – Gut

The Microbiome of Aging and Age-Related Disease – 2014 Meeting Abstracts

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – ArXiv.org

Cancer and the microbiome: potential applications as new tumor biomarker – Khan Shahanavaj – Expert Review of Anticancer Therapy

Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Camila S. Cardinelli – Obesity Surgery

Animal models of microbiome research

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

Animal microbiome

Microbiomes, plausible players or not in alteration of host behaviour – David G. Biron – Frontiers in Microbiology

The Howler Monkey as a Model for Exploring Host-Gut Microbiota Interactions in Primates – Katherine R. Amato, Nicoletta Righini – Howler Monkeys

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra) – Katherine R. Amato – Microbial Ecology

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota – T.D.J. Bello González – Beneficial Microbes

Effects of dietary supplementation of a commercial prebiotic Previda® on survival, growth, immune responses and gut microbiota of Pacific white shrimp, Litopenaeus vannamei – J.D. Anuta – Aquaculture Nutrition

Metagenomic-Based Study of the Phylogenetic and Functional Gene Diversity in Galápagos Land and Marine Iguanas – Pei-Ying Hong – Microbial Ecology

Plant microbiome

The plant microbiome at work – Klaus Schlaeppi and Davide Bulgarelli – Molecular Plant-Microbe Interactions

Tree communities rapidly alter soil microbial resistance and resilience to drought – David Rivest – Functional Ecology

The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities – Zheng Zhang – International Journal of Molecular Sciences

Analysis of microbial taxonomical groups present in maize stalks suppressive to colonization by toxigenic Fusarium spp.: A strategy for the identification of potential antagonists – Jürgen Köhl – Biological Control

Soil and sediment microbiome

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland – Raeid M. M. Abed – PLOS ONE

Do climate factors govern soil microbial community composition and biomass at a regional scale? – L. Ma – Biogeosciences Discuss

Water microbiome

Early succession of micro-periphyton communities in kelp bed and barren ground ecological systems – Roberto A. Uribe – Marine Ecology

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China – Shang Wang – Scientific Reports

Effects of warming on microbial communities in the coastal waters of temperate and subtropical zones in the Northern Hemisphere, with a focus on Gammaproteobacteria
Dao Thi Anh Tuyet – Journal of Oceanography

Colonization in the photic zone and subsequent changes during sinking determines bacterial community composition in marine snow – Stefan Thiele – Applied and Environmental Microbiology

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland
Raeid M. M. Abed – PLOS ONE

Bioreactor microbiology

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures – Shaobo Liang – Bioresource Technology

A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates – Damian E. Helbling – Water Research

Metagenomics

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India – Johan Bengtsson-Palme – Frontiers in Microbiology

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity – Michelle Davison – Photosynthesis Research

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLIFE

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing – Alexander W. Eastman and Ze-Chun Yuan – Frontiers in Microbiology

Metabolomics and transcriptomics

Terpene synthases are widely distributed in bacteria – Yuuki Yamada – PNAS USA

Scaling microbial biomass, metabolism and resource supply – Robert L. Sinsabaugh – Biogeochemistry

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume – Jason A Hilton – ISME Journal

Mining Soil Metagenomes to Better Understand the Evolution of Natural Product Structural Diversity: Pentangular Polyphenols as a Case Study – Hahk-Soo Kang and Sean F. Brady – Journal of the American Chemical Society

Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale – Darrell W. Cockburn – Molecular Microbiology

Techniques

Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory – Yolanda Blanco – PLOS ONE

Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing – Annette Carola Anderson – BMC Microbiology

Probiotics

Probiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis – Susana Delgado – Frontiers in Microbiology

Phages and viruses

Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – E. Saussereau – Clinical Microbiology and Infection

More Microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeldemail, Onur Erbilgin – Trends in Microbiology

The impact of triclosan on the spread of antibiotic resistance in the environment – Daniel E. Carey – Frontiers in Microbiology

Microbes in the news

At Last, I Meet My Microbes – Katherine Harmon Courage – NPR Shots

This Is Your Microbiome: Katherine Harmon Courage at NPR is taking a tour through her microbiome and that of her husband, mother, and dog, as she recounts in a four-part series – Genome Web

Big Idea 2015: Medicine, Wellbeing, and the Microbiome – Deepak Chopra – LinkedIn

When Threatened By Worms, Bacteria Summon Killer Fungi – Ed Yong – National Geographic

Parkinson’s disease linked to gut bacteria – Tim Sandle – Digital Journal

Bacteria in 550-million-year-old fossils provide new clues about fossil formation – Science Codex

Yellowstone Thermal Pools Colored by Pollution – Patrick J Kiger – Discovery

Floating Toilets That Clean Themselves Grow On A Lake – Nsikan Akpan – NPR Goats and Soda

Bettendorf wrestling coach’s invention tackles germs and bacteria on sporting mats and floors – Dennis Moran – QC Online

People on Craigslist Want to Give You Bacteria for Free – Natalie Kitroeff – BusinessWeek

Science, publishing, career

Patterns of text reuse in a scientific corpus – Daniel T. Citron and Paul Ginsparg – PNAS USA

The Anti-Plagiarism Machine: An analysis of hundreds of thousands of scientific papers finds text re-use is rampant, but it isn’t always malicious – Adrienne Lafrance – The Atlantic

“You Are Welcome Here”: Small Stickers Make a Big Difference for LGBTQ Scientists – Kyle Frischkorn – Scientific American

Science and Art

Incredible Bacteria-Laced Fabric Combines Art, Biology And Fashion – Priscilla Frank – Huffington Post
Bik’s Picks

Evolutionary perspectives on human height variation – Gert Stulp and Louise Barrett – Biological Reviews

What the ‘marshmallow test’ can teach you about your kids – Chuck Hadad – CNN

7 of the Ocean’s Strangest Creatures, Including a Fish With a Flashlight – Matt Simon – Wired

Modern genetics confirm ancient relationship between fins and hands – Science Daily

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December 19, 2014

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Pregnancy and Birth

Lots of abstracts (mostly from the group of Kjersti Aagaard) from the 35th Annual Meeting of the Society for Maternal-Fetal Medicine — The Pregnancy Meeting in the American Journal of Obstetrics and Gynecology

13: Association of preterm birth with alterations in the microbiome and linkage to host mtDNA variants – Kjersti Aagaard

57: Alterations in the intestinal microbiome of infants are associated with breastfeeding practice – Derrick Chu

78: Distinct alterations in the placental microbiome among spontaneous preterm births – Kjersti Aagaard

79: Metagenomics of a population-based prospective cohort reveals no discernable impact of mode of delivery (MOD) on the infant microbiome by 6 weeks of age – Derrick Chu

122: The microbiome of the placenta is altered among subjects with severe chorioamnionitis & spontaneous preterm birth – Amanda Prince

282: Chorioamnionitis induced by intramniotic injection of IL1, LPS or Ureaplasma parvum is associated with an altered microbiome in a primate model of inflammatory preterm birth (PTB) – Amanda Prince

283: Amniotic fluid microbiome community and inflammation in women with second trimester cervical changes – Amanda Roman

342: Poor maternal nutrition is associated with alterations in the maternal and neonatal microbiome communities – Kathleen Antony

650: Characterization of the vaginal microbiome following preterm premature rupture of membranes (PPROM) – Janet Hill

709: Race, latency, and fetal membrane microbiota diversity in preterm premature rupture of membranes – Sarahn Wheeler

Human oral microbiome

* Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa – Li J – BMC Microbiology

Human respiratory microbiome

* The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition – Cremers AJ – Microbiome Journal

Human gut microbiome

* The gut microbiota of Colombians differs from that of Americans, Europeans and Asians – Escobar JS – BMC Microbiology

Gut Microbiota: Its Role in Hepatic Encephalopathy – Rahul Rai – Journal of Clinical and Experimental Hepatology

The fungal microbiota of de-novo paediatric inflammatory bowel disease – I. Mukhopadhya – Microbes and Infection

Human vaginal microbiome

Colonization of the upper genital tract by vaginal bacterial species in non-pregnant women  – Caroline M. Mitchell – American Journal of Obstetrics and Gynecology

Transcriptional fingerprints of antigen-presenting cell subsets in the human vaginal mucosa and skin reflect tissue-specific immune microenvironments – Dorothée Duluc – Genome Medicine

Animal models

Microbially Driven TLR5-Dependent Signaling Governs Distal Malignant Progression through Tumor-Promoting Inflammation – Melanie R. Rutkowski – Cancer Cell

Intestinal microbiota diversity and expression of pattern recognition receptors in newly weaned piglets – Xin Tao – Anaerobe

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

The effects of Lactobacillus acidophilus as feed supplement on skin mucosal immune parameters, intestinal microbiota, stress resistance and growth performance of black swordtail (Xiphophorus helleri) – Seyed Hossein Hoseinifar – Fish & Shellfish Immunology

Animal microbiome

Investigation of a new acetogen isolated from an enrichment of the tammar wallaby forestomach – Gagen EJ – BMC Microbiology

Metagenomics, bioinformatics

Determining the quality and complexityof next-generation sequencing data without
a reference genome – Seyed Yahya Anvar – Genome Biology

Techniques

Tracking down the sources of experimental contamination in microbiome studies – Sophie Weiss – Genome Biology

More microbiology

Single cell genomics of bacterial pathogens: outlook for infectious disease research – Jeffrey S McLean and Roger S Lasken – Genome Medicine

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens – Maha R Farhat – Genome Medicine

Environmental enteropathy and malnutrition: do we know enough to intervene? – William A Petri – BMC Medicine

Microbes in the news

Mix of Bacteria in Gut May Depend More on Diet than Genes – Microbiota, Microbiome Change Quickly, UCSF Researchers Find – Jeffrey Norris – UCSF

Protection of the mouse gut by mucus depends on microbes – Phys.org

Life would go on if all bacteria disappeared (but it would totally suck) – Rachel Feltman – Washington Post

New technology using bacteria from dung helps coffee farmers to purify water – Oliver Balch – The Guardian

Science, publishing, career

Dragging scientific publishing into the 21st century – Razib Khan – Genome Biology

Training for peer review: why we need it and how to get there – David Moher – Biome BioMedCentral

Along with the privilege of authorship come important responsibilities – David Moher – BMC Medicine

Crashing the Old Boys’ Science Club – Yamina Berchiche – Live Science

Bik’s Picks

‘People Can Be Afraid of Anything’ – There are plenty of people afraid of whales who will never even see one. How I learned about, and tried to conquer, my own cetaphobia – Kate Horowitz – The Atlantic

Playlist: Science! – NPR/TED staff – NPR

Birds sensed severe storms and fled before tornado outbreak – Science Daily

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December 17, 2014

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A late digest today – I have been busy writing a paper and cooking for our lab’s annual holiday potluck party tomorrow. But here we go:

Human gut microbiome

Complex host genetics influence the microbiome in inflammatory bowel disease – Dan Knights – Genome Medicine

Microbiota and the human nature: know thyself – Harald Brüssow – Environmental Microbiology

Animal and bioreactor models of microbiome

Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model – Julie A.K. McDonald – Journal of Microbiological Methods

A novel method to characterize bacterial communities affected by carbon source and electricity generation in microbial fuel cells using stable isotope probing and Illumina sequencing – Yang Song – Journal of Microbiological Methods

Animal microbiome
Crab: Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents – Katrin Zwirglmaier – MicrobiologyOpen

Soil microbiome

Minireview: The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria – Joseph Nesme and Pascal Simonet – Environmental Microbiology

The soil microbial community predicts the importance of plant traits in plant–soil feedback – Po-Ju Ke – New Phytologist

Metagenomics

Tle distribution and diversity in metagenomic datasets reveal niche specialization – Frank Egan – Environmental Microbiology Reports

Techniques

Application of a single-colony coculture technique to the isolation of unculturable gut bacteria – Yoshiki Tanaka – Microbiology and Immunology

A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria – Christian Strauss – Journal of Microbiological Methods

Microbial Ecology

Microbial biogeography: the end of the ubiquitous dispersal hypothesis? – Christopher J. van der Gast – Environmental Microbiology

Bacteria can mobilize nematode-trapping fungi to kill nematodes – Xin Wang – Nature Communications

Microfluidic single-cell analysis links boundary environments and individual microbial phenotypes – Christian Dusny and Andreas Schmid – Environmental Microbiology

Microbes in the News

Microbiome may have shaped early human populations – Phys.org

Commensal bacteria were critical shapers of early human populations – Phys.org

Microbes played a significant role in human evolution, study says – Chuck Bednar – RedOrbit

The microbes we eat: Study investigates bacteria in different diets – Nathan Gray – NutraIngredients

Researchers source stool samples to study gut bacteria – Nicole Kwan – FOX News

Bacterial biofilms are associated with colon cancer, imaging technique reveals – Science Daily

Do Autoimmune Diseases Begin in the Gut? – Stephen Paget – Medscape

People may inherit ‘gut’ bacteria that cause Crohn’s disease and ulcerative colitis – MedicalXpress

* 2015 will be the year of the Microbiome (and 28 other predictions) – Fortune

#BacteriaHysteria: The hidden dangers lurking in your kitchen: Chopping boards harbour 200% more faecal bacteria than toilet seats and potatoes and leeks can give you food poisoning – Lizzie Parry – Daily Mail Online

Scientists Debate If It’s OK To Make Viruses More Dangerous In The Lab – Nell Greenfieldboyce – NPR Shots Health News

Science, publishing, and career

12 Unimpressed Comments From Peer Reviewers – Kristy Hamilton – IFL Science (for more entertaining quotes in Environmental Microbiology, see here)

Journalists to Catalog Retractions: Staff of the blog Retraction Watch will create a database of papers retracted from the scientific literature – Kerry Grens – The Scientist

Here’s What Happens When Female MIT PhDs Do a Reddit AMA About Computer Science – Lauren Landry – BostInno

How to be a science girl in a Barbie world – Eve Andrews – Grist.org

For Sale: “Your Name Here” in a Prestigious Science Journal – Charles Seife – Scientific American

These Beautiful Women in Science Art Prints Feature Rad As Heck Ladies – Sam Maggs – The Mary Sue

Bik’s Picks

Happy Holidays from the Corals! – Ocean Portal – Smithsonian

Science’s good, bad, ugly year – Tom Siegfried – Science News

Meet Bill Nye, The Anti-Science Guy – Robert Tracinski – The Federalist

10 Cutest Animals in Science in 2014 – Megan Gannon – Live Science

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December 12, 2014

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Human oral microbiome

Periodontal microbiology in Latin America – Adolfo Contreras – Periodontology 2000

Current perspective of the impact of smoking on the progression and treatment of periodontitis – Francisco H. Nociti Jr – Periodontology 2000

Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses – Néstor J. López, Sergio Uribe and Benjamín Martinez – Periodontology 2000

Pregnancy and birth

* The Infant Microbiome Development: Mom Matters – Noel T. Mueller – Trends in Molecular Medicine

(see also above) Effect of periodontal treatment on preterm birth rate: a systematic review of meta-analyses – Néstor J. López, Sergio Uribe and Benjamín Martinez – Periodontology 2000

Pre- and probiotics, functional foods

Repeated cooking and freezing of whole wheat flour increases resistant starch with beneficial impacts on in vitro fecal fermentation properties – Jennifer A. Arcila, Devin J. Rose – Journal of Functional Foods

Potential of cereal grains and grain legumes in modulating pigs’ intestinal microbiota – A review – Tobias Aumiller – Livestock Science

Significance of Inulin Fructans in the Human Diet – Gertjan Schaafsma and Joanne L. Slavin – Comprehensive Reviews in Food Science and Food Safety

Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults – Edward S Chambers – Gut

Animal models

P47 – A dietary-driven redox modulation of gut microbiome-host interactions: the rescue of epithelial barrier and mucus production during dysbiosis by dietary nitrate – Bárbara Rocha – Free Radical Biology and Medicine

Dietary Pectin–Derived Acidic Oligosaccharides Improve the Pulmonary Bacterial Clearance of Pseudomonas aeruginosa Lung Infection in Mice by Modulating Intestinal Microbiota and Immunity – Henry Bernard – The Journal of Infectious Diseases

Soil microbiome

Response of autochthonous microbiota of diesel polluted soils to land-farming treatments – Gloria Andrea Silva-Castro – Environmental Research

Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective – Pablo García-Palacios – Global Change Biology

Experimental evaluation of CO2 percolation effects on subsurface soil microbiota –
Patricia Österreicher-Cunha – International Journal of Greenhouse Gas Control

Water microbiome

In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs – Maria G. Pachiadaki – Deep Sea Research Part II: Topical Studies in Oceanography

Metabolomics

Microbial Urease in Health and Disease – Diego Mora, Stefania Arioli – PLOS Pathogens

Bioinformatics

“Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education – Yang Ding – PLOS Computational Biology

Techniques
Effect of Two Different Commercial DNA Extraction Kits on the Bacterial 16S rRNA gene Denaturing Gradient Gel Electrophoresis Profile of Arabian Gelding Feces – Megan L. Shepherd – Journal of Equine Veterinary Science

More microbiology papers

mBio Addresses the Pause in Gain-of-Function (GOF) Experiments Involving Pathogens with Pandemic Potential (PPP) – Arturo Casadevall – mBio

The battle for iron – Andrew E. Armitage, Hal Drakesmith – Science

Bacteriophage exclusion, a new defense system – Rodolphe Barrangou and John van der Oost – The EMBO Journal

Microbes in the news

Poo And You: A Journey Into The Guts Of A Microbiome – Katherine Harmon Courage – NPR Health

The Gut and Arthritis: The Evidence Grows – Nancy Walsh and Diana Swift – MedPageToday

Gross! Apparently Your Bacteria Is What Makes or Breaks a Relationship? – Zahra Barnes – Glamour.com (who knew?)

A Powder Made From Bacteria Waste Could Curb Overeating – Sarah Zhang – Gizmodo

Science, publishing, career

Scientific Elevator Pitches: A number of competitions around the world are challenging young scientists to describe their research in mere minutes – Rina Shaikh-Lesko – The Scientist

More science doctorates, fewer postdoctorate science jobs – Beryl Lieff Benderly – Science Careers

Making science a desirable career – Jessica K. Polka, Kristin A. Krukenberg – Science Magazine

Tips for Talking to Politicians: Members of an American Society for Cell Biology panel urge their colleagues to consider science advocacy – Tracy Vence – The Scientist

What Should High School Students Learn About Science? – Ria Misra – Space io9

Faculty member leads development of webinars that improve science education – Samantha Schwartz – PennState News

In defamation case, PubPeer moves to quash subpoena to unmask anonymous commenters – Kelly Servick – Science Magazine

Scientific American’s Top 10 Science Stories of 2014 – Scientific American

Bik’s Picks

Why whale poo matters – George Monbiot – The Guardian

Introduction to special Science Issue on bird genomes: A flock of genomes – Guojie Zhang – Science

The Darwin Awards: sex differences in idiotic behaviour – Ben Alexander Daniel Lendrem – British Medical Journal

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December 11, 2014

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The Bay Area is getting drenched with rain right now, and several leaks in our roof kept me busy with buckets and towels, but the power is still on, so here we go:

Human microbiome general

* Review: The demographic determinants of human microbiome health – Sylvie Estrela – Trends in Microbiology

Human oral microbiome

Salivary Mucins Protect Surfaces from Colonization by Cariogenic Bacteria – Erica Shapiro Frenkel – Applied and Environmental Microbiology

Human gut microbiome

* Effects of the gut microbiota on bone mass – Claes Ohlsson, Klara Sjögren – Trends in Endocrinology & Metabolism

Discovery of a Conjugative Megaplasmid in Bifidobacterium breve – Francesca Bottacini – Applied and Environmental Microbiology

Microbiome of pregnancy and birth

Microbiome of the placenta in pre-eclampsia supports the role of bacteria in the multifactorial cause of pre-eclampsia – Ranmalee Amarasekara – Journal of Obstetrics and Gynaecology Research
Animal and bioreactor models

Optimization of a rapid and efficient analytical pipeline for in-depth metaproteome characterization: evaluation on mock microbial mixtures and application to the mouse gut microbiome – Alessandro Tanca – Microbiome

* Microbial shifts in the aging mouse gut – Morgan GI Langille – Microbiome

Development of human colonic microbiota in the computer-controlled dynamic SIMulator of the GastroIntestinal tract SIMGI – Elvira Barroso – LWT – Food Science and Technology

Protocols for Microcosms for Growing Biofilms on Hydrophobic Substrates: A Polyphasic Approach to Study Biodiversity, Metabolic Activity, and Biofilm Architecture – Wolf-Rainer Abraham – Springer Protocols Handbooks 2014

Animal microbiome

Acidobacteria appear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid – Aileen O¿Connor-Sánchez – Biological Research

Plant microbiome

The impact of systemic and copper pesticide applications on the phyllosphere microflora of tomatoes – Andrea R Ottesen – Journal of the Science of Food and Agriculture

Soil and sediment microbiome

Linkages between the soil organic matter fractions and the microbial metabolic functional diversity within a broad-leaved Korean pine forest – Jing Tian – European Journal of Soil Biology

Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests – Karina E. Clemmensen – New Phytologist

Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge – Sean Storey – Bioresource Technology

Water microbiome

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination – Alice C. Ortmann – Marine Pollution Bulletin

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination – Alice C. Ortmann, YueHan Lu – Marine Pollution Bulletin

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany) – Andreas Oikonomou – Environmental Microbiology

Exploration of Microbial Diversity of Taptapani (India) Hot Spring Through Molecular Phylogenetic Analysis – Sudip Kumar Sen – Arabian Journal for Science and Engineering

Food microbiology

Selection of Autochthonous Strains as Starter Cultures for Fermented Fish Products – Barbara Speranza – Journal of Food Science

Microbes in the news

Pregnancy Germs: Friend Or Foe? – How The Maternal Microbiome Influences Pregnancy Health – PR NewsWire / March of Dimes

Study Hints Gut Microbiome Plays A Role in Multiple Sclerosis –
Kate O’Rourke – Gastroenterology and Endoscopy News

“The Great Plate Count Anomaly” that is no more – Gemma Reguera – Small Things Considered ASM

Google Science Fair – Bacteria boosting cereal crop yields – Brett Worthington – ABC Net Australia

Guts of obese dogs look similar to those of obese people – Agata Blaszczak-Boxe – Science Magazine

Baby infected in birthing pool died of Legionnaire’s disease – Bahar Gholipour – CBS News

Science, publishing, and career

Scientists Often Skip A Simple Test That Could Verify Their Work – NPR Morning Edition

Study of massive preprint archive hints at the geography of plagiarism – John Bohannon – Science Insider

Bik’s Picks

Deep Neural Networks are Easily Fooled: High Confidence Predictions for Unrecognizable Images – Anh Nguyen – Arxiv

Three-in-one drug cuts body weight by a third – Nsikan Akpan – Science Magazine

Water vapor on Rosetta’s target comet significantly different from that found on Earth – Science Daily

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December 10, 2014

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Food microbiome

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types – Jenna M. Lang – PeerJ

Human oral microbiome

Subgingival microbial profiles of Sudanese patients with aggressive periodontitis – H. R. Z. Elabdeen – Journal of Periodontal Research

Human bladder microbiome

Interplay between Bladder Microbiota and Urinary Antimicrobial Peptides: Mechanisms for Human Urinary Tract Infection Risk and Symptom Severity – Vanessa Nienhouse – PLOS ONE

Human gut microbiome

Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota – Bartholomeus van den Bogert – PLOS ONE

Animal models of microbiome research

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape – Meredith M. Curtis – Cell Host & Microbe

Gut Microbiota-Produced Succinate Promotes C. difficile Infection after Antibiotic Treatment or Motility Disturbance – Jessica A. Ferreyra – Cell Host & Microbe

Regionally Distinct Alterations in the Composition of the Gut Microbiota in Rats with Streptozotocin-Induced Diabetes – Roland Wirth – PLOS ONE

Animal microbiome

Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture – Yeojun Yun – PLOS ONE

Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus) – Zhipeng Li – PLOS ONE

Transcriptomic Immune Response of the Cotton Stainer Dysdercus fasciatus to Experimental Elimination of Vitamin-Supplementing Intestinal Symbionts – Eugen Bauer – PLOS ONE

Metabolomics

Stool Phospholipid Signature is Altered by Diet and Tumors – Julie M. Davies – PLOS ONE

Pathogens’ Exploitation of the Intestinal Food Web
Tu Anh Pham N., Trevor D. Lawley – Cell Host & Microbe

Could resistant starch be the redeemer of dietary carbohydrate? – M Denise Robertson – Practical Diabetes

A New Insight into the Physiological Role of Bile Salt Hydrolase among Intestinal Bacteria from the Genus Bifidobacterium – Piotr Jarocki – PLOS ONE

Metagenomics

Maths on microbes: adding microbial ecophysiology to metagenomics – Wilfred F. M. Röling – Microbial Biotechnology

Functional optimization of gene clusters by combinatorial design and assembly – Michael J Smanski – Nature Biotechnology

More microbiology

Microbiology: Ditch the term pathogen – Arturo Casadevall & Liise-anne Pirofski – Nature

New sequencing technique: MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island – Philip M Ashton – Nature Biotechnology

Microbes in the news

NASA ISS On-Orbit Status 5 December 2014: Microbiome Experiment – SpaceRef

Bacteria’s Game of ‘Telephone’ Foils Microbiologists’ Eavesdropping – Kim Krieger – UConnToday

Science, publishing, career

The Point When Science Becomes Publicity – James Hamblin – The Atlantic

No Lovin’ Feeling… for Science Fair – Claire Wapole – Huffington Post

How to cope when things go wrong in academia – Julie Gould – Nature Jobs

Scientific Peer Review Is Broken. We’re Fighting to Fix It With Anonymity – The Founders of PubPeer – Wired.com

Not sure how old this is, but I liked the graph: The illustrated guide to a Ph.D. – Matt Might

Ocean biology: Marine dreams – Chris Woolston – Nature

New postdoc report covers familiar ground – Beryl Lieff Benderly, Jim Austin – Science Careers

Bik’s Picks

Injectable 3-D vaccines could fight cancer, infectious diseases – ScienceDaily

Glittering Nobel Gown Represents Scientist’s Work – Joanne Manaster – Scientific American

This Commuter Bus Runs On Poop- A U.K.-based biogas plant has developed a 40-seater than runs on converted sewage and food waste – Corinne Iozzio – Smithsonian

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