The Escherichia coli transcriptome mostly consists of independently regulated modules

Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome

Vasospasm in children with traumatic brain injury

To determine the incidence of vasospasm in children who have suffered moderate to severe traumatic brain injury. A prospective observational pilot study in a 24-bed pediatric intensive care unit was performed. Twenty-two children aged 7 months to 14 years with moderate to severe traumatic brain injury as indicated by Glasgow Coma Score ≤12 and abnormal head imaging were enrolled. Transcranial Doppler ultrasound was performed to identify and follow vasospasm. Patients with a flow velocity in the middle cerebral artery (MCA) >120 cm/s were considered to have vasospasm by criterion A. If flow velocity in the MCA was >120 cm/s and the Lindegaard ratio was >3, vasospasm was considered to be present by criterion B. Patients with basilar artery (BA) flow velocity >90 cm/s met criteria for vasospasm in the posterior circulation (criterion C). In the MCA, 45.5% of patients developed vasospasm based on criterion A and 36.3% developed vasospasm based on criterion B. A total of 18.2% of patients developed vasospasm in the BA by criterion C. Typical day of onset of vasospasm was hospital day 2–3. Duration of vasospasm in the anterior circulation was 4 ± 2 days based on criteria A and 3 ± 1 days based on criteria B. Vasospasm in the posterior circulation persisted for 2 ± 1 days. Using the adult criteria outlined above to diagnose vasospasm, a significant proportion of pediatric patients who have suffered moderate to severe traumatic brain injury develop vasospasm during the course of their treatment

The swimming kinematics of larval Atlantic cod, Gadus morhua L., are resilient to elevated seawater pCO2

Kinematics of swimming behavior of larval Atlantic cod, aged 12 and 27 days post-hatch (dph) and cultured under three pCO2 conditions (control-370, medium-1800, and high-4200 μatm) from March to May 2010, were extracted from swim path recordings obtained using silhouette video photography. The swim paths were analyzed for swim duration, distance and speed, stop duration, and horizontal and vertical turn angles to determine whether elevated seawater pCO2—at beyond near-future ocean acidification levels—affects the swimming kinematics of Atlantic cod larvae. There were no significant differences in most of the variables tested: the swimming kinematics of Atlantic cod larvae at 12 and 27 dph were highly resilient to extremely elevated pCO2 levels. Nonetheless, cod larvae cultured at the highest pCO2 concentration displayed vertical turn angles that were more restricted (median turn angle, 15°) than larvae in the control (19°) and medium (19°) treatments at 12 dph (but not at 27 dph). Significant reduction in the stop duration of cod larvae from the high treatment (median stop duration, 0.28 s) was also observed compared to the larvae from the control group (0.32 s) at 27 dph (but not at 12 dph). The functional and ecological significance of these subtle differences are unclear and, therefore, require further investigation in order to determine whether they are ecologically relevant or spurious

Green Criminology Before ‘Green Criminology’: Amnesia and Absences

Although the first published use of the term ‘green criminology’ seems to have been made by Lynch (Green criminology. Aldershot, Hampshire, 1990/2006), elements of the analysis and critique represented by the term were established well before this date. There is much criminological engagement with, and analysis of, environmental crime and harm that occurred prior to 1990 that deserves acknowledgement. In this article, we try to illuminate some of the antecedents of green criminology. Proceeding in this way allows us to learn from ‘absences’, i.e. knowledge that existed but has been forgotten. We conclude by referring to green criminology not as an exclusionary label or barrier but as a symbol that guides and inspires the direction of research

Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas

Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.SCOPUS: ar.jinfo:eu-repo/semantics/publishe