Artificial Polyploidy Improves Bacterial Single Cell Genome Recovery

BACKGROUND: Single cell genomics (SCG) is a combination of methods whose goal is to decipher the complete genomic sequence from a single cell and has been applied mostly to organisms with smaller genomes, such as bacteria and archaea. Prior single cell studies showed that a significant portion of a genome could be obtained. However, breakages of genomic DNA and amplification bias have made it very challenging to acquire a complete genome with single cells. We investigated an artificial method to induce polyploidy in Bacillus subtilis ATCC 6633 by blocking cell division and have shown that we can significantly improve the performance of genomic sequencing from a single cell. METHODOLOGY/PRINCIPAL FINDINGS: We inhibited the bacterial cytoskeleton protein FtsZ in B.subtilis with an FtsZ-inhibiting compound, PC190723, resulting in larger undivided single cells with multiple copies of its genome. qPCR assays of these larger, sorted cells showed higher DNA content, have less amplification bias, and greater genomic recovery than untreated cells. SIGNIFICANCE: The method presented here shows the potential to obtain a nearly complete genome sequence from a single bacterial cell. With millions of uncultured bacterial species in nature, this method holds tremendous promise to provide insight into the genomic novelty of yet-to-be discovered species, and given the temporary effects of artificial polyploidy coupled with the ability to sort and distinguish differences in cell size and genomic DNA content, may allow recovery of specific organisms in addition to their genomes

Correction:How the COVID-19 pandemic highlights the necessity of animal research (vol 30, pg R1014, 2020)

(Current Biology 30, R1014–R1018; September 21, 2020) As a result of an author oversight in the originally published version of this article, a number of errors were introduced in the author list and affiliations. First, the middle initials were omitted from the names of several authors. Second, the surname of Dr. van Dam was mistakenly written as “Dam.” Third, the first name of author Bernhard Englitz was misspelled as “Bernard” and the surname of author B.J.A. Pollux was misspelled as “Pullox.” Finally, Dr. Keijer's first name was abbreviated rather than written in full. These errors, as well as various errors in the author affiliations, have now been corrected online

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

REGIONAL DEMOGRAPHIC IMPACTS on DRIVERS of SOCIAL VULNERABILITY: A LOCAL VIEW of NORWAY

The combination of climate projections for Norway, and its recent demographic history make the country a good case study for regional development and social vulnerability to climate change. The rural settlements constituting northern Norway maintain an economic and demographic history with the potential to create a scenario of regional social vulnerability. The paper's analysis will illustrate the great variation between the regions of northern and southern Norway. This paper's objective is to assess Norway's potential for social vulnerability to climate change at a more local level.Thesis (M.S., Geography) -- University of Idaho, December 201

Climatic Variability in the Southwest Pacific During the Last Termination (20-10 Kyr BP)

The degree to which palaeoclimatic changes in the Southern Hemisphere co-varied with events in the high latitude Northern Hemisphere during the Last Termination is a contentious issue, with conflicting evidence for the degree of 'teleconnection' between different regions of the Southern Hemisphere. The available hypotheses are difficult to test robustly, however, because there are few detailed palaeoclimatic records in the Southern Hemisphere. Here we present climatic reconstructions from the southwestern Pacific, a key region in the Southern Hemisphere because of the potentially important role it plays in global climate change. The reconstructions for the period 20-10 kyr BP were obtained from five sites along a transect from southern New Zealand, through Australia to Indonesia, supported by 125 calibrated 14C ages. Two periods of significant climatic change can be identified across the region at around 17 and 14.2 cal kyr BP, most probably associated with the onset of warming in the West Pacific Warm Pool and the collapse of Antarctic ice during Meltwater Pulse-1A, respectively. The severe geochronological constraints that inherently afflict age models based on radiocarbon dating and the lack of quantified climatic parameters make more detailed interpretations problematic, however. There is an urgent need to address the geochronological limitations, and to develop more precise and quantified estimates of the pronounced climate variations that clearly affected this region during the Last Termination

Increased rates of invasive bacterial disease in late 2022

Invasive bacterial disease is associated with significant morbidity and mortality. In winter 2022, there was an apparent increased rate of invasive bacterial disease compared to preceding years. Cross-site retrospective analysis of the three Children's Health Ireland (CHI) hospitals looking at children admitted between 1st October 2022-31st December 2022 (Q4) with community-acquired invasive bacterial disease, defined as an abscess in a normally sterile site in the head, neck and chest or isolation or PCR detection of Streptococcus pneumoniae, Neisseria meningitidis, Streptococcus pyogenes (Group A streptococcus) or Haemophilus influenzae from a normally sterile site. Case numbers were compared to Q4 in each of 2018-2021. Eighty-two children met the case definition in Q4 2022 vs 97 (Q4 2018-2021). In 2022, 42/82 (51%) were female, median age 3.75 years (1.5-8.25 years). Only 2 (2%) were immunosuppressed and 2 others (2%) had underlying neurodisability. Fifty (61%) were admitted on second or subsequent presentation to a healthcare setting. Fifty-six (68%) had an abscess in a sterile site. Bloodstream infection (positive blood culture or PCR: 24 (29%)) was the most common site of infection, followed by neck 22 (27%) and intracranial 12 (15%). Group A streptococcus (GAS) 27 (33%) was the most common organism isolated. Seven cases (9%) died in 2022 compared to 2 patients (2%) from 2018 to 2021 (p 1 in 2022 than 2018-2021 (p = 0.003). Conclusion: Invasive bacterial diseases increased in Q4 2022 with higher morbidity and mortality than in the preceding 4 years. Group A streptococcal infection was the most significant organism in 2022.  What is known: • Invasive bacterial disease is the leading cause of childhood mortality globally. • There was an increase in cases of invasive Group A streptococcus infections reported in many countries (including Ireland) during the winter of 2022/23.  What is new: • Head, neck and chest abscesses increased in Q4 of 2022 compared to the previous 4 years combined. • Invasive bacterial infections in Q4 of 2022 were associated with higher rates of mortality (9%), paediatric intensive care unit (PICU) admission (24%) and requirement for surgical drainage or intervention (67%) than in the preceding years.</p

Australia's biodiversity crisis and the need for the Biodiversity Council

Australia is a mega-biodiverse region. Millions of years of geographical isolation have resulted in high species diversity and endemism. So far, &gt;21 000 species of plants, 8000 species of vertebrates, and 110 000 species of insects and other invertebrates have been described (Chapman 2009). An exceptionally high percentage are endemic; 93% of flowering plants, &gt;80% of invertebrates, 87% of mammals, 93% of reptiles, 94% of frogs, 74% of freshwater fishes and &gt;50% of temperate marine fishes in Australia are found nowhere else (Lintermans 2013; Cresswell &amp; Murphy 2017)