Writing in your own voice: An intervention that reduces plagiarism and common writing problems in students' scientific writing.

In many of our courses, particularly laboratory courses, students are expected to engage in scientific writing. Despite various efforts by other courses and library resources, as instructors we are often faced with the frustration of student plagiarism and related writing problems. Here, we describe a simple Writing in Your Own Voice intervention designed to help students become more aware of different types of plagiarism and writing problems, avoid those problems, and practice writing in their own voice. In this article, we will introduce the types of plagiarism and writing problems commonly encountered in our molecular biology laboratory course, the intervention, and the results of our study. From the evaluation of 365 student reports, we found the intervention resulted in nearly 50% fewer instances of plagiarism and common writing problems. We also observed significantly fewer instances of severe plagiarism (e.g. several sentences copied from an external source). In addition, we find that the effects last for several weeks after the students complete the intervention assignment. This assignment is particularly easy to implement and can be a very useful tool for teaching students how to write in their own voices. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):589-598, 2019

Fishery Associated Changes in the Whelk Buccinum undatum Stock in the Southwest Irish Sea, 1995-2003

The whelk fishery of the southwest Irish Sea had a turnover of approximately €18 million and employed 250 people directly and indirectly in catching and processing in 2003. In the nine years, 1995-2003 inclusive, whelk landings to Ireland from the southwest Irish Sea fluctuated between 3,800 and almost 10,000 tonnes(t) per year; from an estimated 5,000 – 15,000 boat-days annually. A collapse in landings was recorded in 1997 and again in the spring of 2004. The fishery is divided for assessment purposes into four sectors, the central two consisting largely of nursery area and the north and south extremities of the fishery populated by more older, larger and mature whelk. Logbooks were not completed by fishermen participating in this fishery which was, in theory, managed by size limit, but the regulations were not enforced. Boats fishing whelk made daily fishing trips and daily weights recorded by processors were used to estimate biomass in each of the sectors by depletion regressions. Total biomass fluctuated between 12,720 t in 1999 and 37,319 t in 2002. The estimates based on a full season’s landings are used to compare the fishery from one year to the next and to supply weighting factors for other parameters of the population. Exploitation rates were lowest in one of the central sectors of the fishery (where they averaged 27% annually). At the southern extremity they averaged 39%. Depletion estimates based on landings records from approximately April to 15 June provided higher exploitation rates and lower biomass. The mortality coefficient Z, calculated from a catch curve, peaked in two years, 1998 and 2002, as did an index of recruitment. The age at full recruitment declined after 2000. Throughout nine years of documented history, one of the central sectors of the fishery assumed progressively greater dominance over the others, providing 77% of the landings from the entire fishery to its ports in 2003. Some sectoral changes to the whelk population may be irreversible: the oldest animals have been removed from the northern extremity of the fishery and while the whelks which are exploited at the southern end between 2000 and 2003 were similar in size to those exploited in the mid-1990s, their tonnage between 1999 and 2003 decreased from 47 to 4% of the landings in 1995. A substantial recruitment in 2001 or 2002 was followed by an increase in fishing effort of 42% between 2002 and 2003 and this is identified as the reason for the collapse in 2004.Funder: Marine Institut

Wheat drought tolerance in the field is predicted by amino acid responses to glasshouse-imposed drought

Water limits crop productivity, so selecting for a minimal yield gap in drier environments is critical to mitigate against climate change and land-use pressure. We investigated the responses of relative water content (RWC), stomatal conductance, chlorophyll content, and metabolites in flag leaves of commercial wheat (Triticum aestivum L.) cultivars to three drought treatments in the glasshouse and in field environments. We observed strong genetic associations between glasshouse-based RWC, metabolites, and yield gap-based drought tolerance (YDT; the ratio of yield in water-limited versus well-watered conditions) across 18 field environments spanning sites and seasons. Critically, RWC response to glasshouse drought was strongly associated with both YDT (r2=0.85, P<8E-6) and RWC under field drought (r2=0.77, P<0.05). Moreover, multiple regression analyses revealed that 98% of genetic YDT variance was explained by drought responses of four metabolites: Serine, asparagine, methionine, and lysine (R2=0.98; P<0.01). Fitted coefficients suggested that, for given levels of serine and asparagine, stronger methionine and lysine accumulation was associated with higher YDT. Collectively, our results demonstrate that high-throughput, targeted metabolic phenotyping of glasshouse-grown plants may be an effective tool for selection of wheat cultivars with high field-derived YDT.We acknowledge the support of the Research School of Biology/Research School of Chemistry Joint Mass Spectrometry Facility and Diversity Arrays Technology, ACT, Australia and financial support by the Grains Research and Development Corporation Grant (ANU00020), Australian Research Council Centre of Excellence for Translational Photosynthesis (CE140100015), and Plant Energy Biology (CE140100008)

Chromosomal Integration of the Klebsiella pneumoniae carbapenemase gene (blaKPC) in Klebsiella Species: Elusive but not Rare

Carbapenemase genes in Enterobacteriaceae are mostly described as being plasmid-associated. However, the genetic context of carbapenemase genes is not always confirmed in epidemiological surveys, and the frequency of their chromosomal integration is therefore unknown. A previously sequenced collection of blaKPC-positive Enterobacteriaceae from a single US institution (2007 2012; n=281 isolates, 182 patients) was analyzed to identify chromosomal insertions of Tn4401, the transposon most frequently harboring blaKPC. Using a combination of short- and long-read sequencing, we confirmed five independent chromosomal integration events from 6/182 (3%) patients, corresponding to 15/281 (5%) isolates. Three patients had isolates identified by peri-rectal screening and three had infections which were all successfully treated. When a single copy of blaKPC was in the chromosome one or both of the phenotypic carbapenemase tests were negative. All chromosomally integrated blaKPC were from Klebsiella spp., predominantly K. pneumoniae clonal group (CG)258, even though these represented only a small proportion of the isolates. Integration occurred via IS15-ΔI mediated transposition of a larger, composite region encompassing Tn4401 at one locus of chromosomal integration, seen in the same strain (K. pneumoniae ST340) in two patients. In summary, we identified five independent chromosomal integrations of blaKPC in a large outbreak, demonstrating that this is not a rare event. blaKPC was more frequently integrated into the chromosome of epidemic CG258 K. pneumoniae lineages (ST11, ST258, ST340), and was more difficult to detect by routine phenotypic methods in this context. The presence of chromosomally integrated blaKPC within successful, globally disseminated K. pneumoniae strains is therefore likely underestimated

Wnt4 is essential to normal mammalian lung development

AbstractWnt signaling is essential to many events during organogenesis, including the development of the mammalian lung. The Wnt family member Wnt4 has been shown to be required for the development of kidney, gonads, thymus, mammary and pituitary glands. Here, we show that Wnt4 is critical for proper morphogenesis and growth of the respiratory system. Using in situ hybridization in mouse embryos, we identify a previously uncharacterized site of Wnt4 expression in the anterior trunk mesoderm. This expression domain initiates as early as E8.25 in the mesoderm abutting the tracheoesophageal endoderm, between the fusing dorsal aortae and the heart. Analysis of Wnt4−/− embryos reveals severe lung hypoplasia and tracheal abnormalities; however, aortic fusion and esophageal development are unaffected. We find decreased cell proliferation in Wnt4−/− lung buds, particularly in tip domains. In addition, we observe reduction of the important lung growth factors Fgf9, Fgf10, Sox9 and Wnt2 in the lung bud during early stages of organogenesis, as well as decreased tracheal expression of the progenitor factor Sox9. Together, these data reveal a previously unknown role for the secreted protein Wnt4 in respiratory system development

Non-detection of HC_(11)N towards TMC-1: constraining the chemistry of large carbon-chain molecules

Bell et al. reported the first detection of the cyanopolyyne HC_(11)N towards the cold dark cloud TMC-1; no subsequent detections have been reported towards any source. Additional observations of cyanopolyynes and other carbon-chain molecules towards TMC-1 have shown a log-linear trend between molecule size and column density, and in an effort to further explore the underlying chemical processes driving this trend, we have analysed Green Bank Telescope observations of HC_9N and HC_(11)N towards TMC-1. Although we find an HC_9N column density consistent with previous values, HC_(11)N is not detected and we derive an upper limit column density significantly below that reported in Bell et al. Using a state-of-the-art chemical model, we have investigated possible explanations of non-linearity in the column density trend. Despite updating the chemical model to better account for ion–dipole interactions, we are not able to explain the non-detection of HC_(11)N, and we interpret this as evidence of previously unknown carbon-chain chemistry. We propose that cyclization reactions may be responsible for the depleted HC11N abundance, and that products of these cyclization reactions should be investigated as candidate interstellar molecules

Non-detection of HC_(11)N towards TMC-1: constraining the chemistry of large carbon-chain molecules

Bell et al. reported the first detection of the cyanopolyyne HC_(11)N towards the cold dark cloud TMC-1; no subsequent detections have been reported towards any source. Additional observations of cyanopolyynes and other carbon-chain molecules towards TMC-1 have shown a log-linear trend between molecule size and column density, and in an effort to further explore the underlying chemical processes driving this trend, we have analysed Green Bank Telescope observations of HC_9N and HC_(11)N towards TMC-1. Although we find an HC_9N column density consistent with previous values, HC_(11)N is not detected and we derive an upper limit column density significantly below that reported in Bell et al. Using a state-of-the-art chemical model, we have investigated possible explanations of non-linearity in the column density trend. Despite updating the chemical model to better account for ion–dipole interactions, we are not able to explain the non-detection of HC_(11)N, and we interpret this as evidence of previously unknown carbon-chain chemistry. We propose that cyclization reactions may be responsible for the depleted HC11N abundance, and that products of these cyclization reactions should be investigated as candidate interstellar molecules

Teleost Growth Factor Independence (Gfi) Genes Differentially Regulate Successive Waves of Hematopoiesis

Growth Factor Independence (Gfi) transcription factors play essential roles in hematopoiesis, differentially activating and repressing transcriptional programs required for hematopoietic stem/progenitor cell (HSPC) development and lineage specification. In mammals, Gfi1a regulates hematopoietic stem cells (HSC), myeloid and lymphoid populations, while its paralog, Gfi1b, regulates HSC, megakaryocyte and erythroid development. In zebrafish, gfi1aa is essential for primitive hematopoiesis; however, little is known about the role of gfi1aa in definitive hematopoiesis or about additional gfi factors in zebrafish. Here, we report the isolation and characterization of an additional hematopoietic gfi factor, gfi1b. We show that gfi1aa and gfi1b are expressed in the primitive and definitive sites of hematopoiesis in zebrafish. Our functional analyses demonstrate that gfi1aa and gfi1b have distinct roles in regulating primitive and definitive hematopoietic progenitors, respectively. Loss of gfi1aa silences markers of early primitive progenitors, scl and gata1. Conversely, loss of gfi1b silences runx-1, c-myb, ikaros and cd41, indicating that gfi1b is required for definitive hematopoiesis. We determine the epistatic relationships between the gfi factors and key hematopoietic transcription factors, demonstrating that gfi1aa and gfi1b join lmo2, scl, runx-1 and c-myb as critical regulators of teleost HSPC. Our studies establish a comparative paradigm for the regulation of hematopoietic lineages by gfi transcription factors.Stem Cell and Regenerative Biolog