In This Issue

doi:10.1073/iti4212109

New Research In

Microbial taxa in deep-sea sediment linked to geochemical variations

Retrieving gravity core from the Arctic Spreading Ridge System. Image courtesy of the Centre for Geobiology, Bergen, Norway.

Marine sediments host the largest reservoir of organic carbon and support the highest microbial abundance on Earth. Though the metabolic processes of these communities profoundly affect global biogeochemical cycles, the physiological activities of most subsurface microorganisms remain largely uncharacterized. Steffen Jørgensen et al. (pp. 16764–16765) report that microbial community structure directly correlates to geochemistry, providing a means to determine factors that shape community composition and predict the metabolic properties of Earth’s most abundant deep-sea sediment microbes. The authors generated an extensive geochemical dataset of microbial profiles from two Arctic Mid-Ocean Ridge system sediment cores and found correlations between changes in the relative abundance of taxonomic groups and geochemical variations. Four key geochemical parameters—total organic carbon, iron content, manganese content, and sulfate concentration in the pore water—were tightly linked to the taxonomic distribution of microorganisms, suggesting that organic carbon and mineral content likely drive microbial community structure and, conversely, community structure likely determines sulfate concentration. The findings help constrain the metabolic regimes of the most abundant prokaryotic organisms in marine sediments, and with further study may lead to models that can predict the long-term fate of carbon and other essential elements, according to the authors. — T.J.

Scientific misconduct to blame for many retractions in the life sciences

Retraction of flawed scientific publications is an important part of the scientific process, serving to correct the scientific literature. Ferric Fang et al. (pp. 17028–17033) conducted a comprehensive review of retracted biomedical and life sciences research articles listed in the PubMed database and found that approximately two-thirds of these retractions were due to some form of misconduct. Of the retractions studied, the authors say 43.4% were retracted due to fraud or suspected fraud, 14.2% due to duplicate publication, 9.8% due to plagiarism, and the rest were retracted because of miscellaneous or unknown reasons. The percentage of scientific articles retracted due to fraud has increased approximately 10-fold since 1975, with a smaller increase in retractions due to error, the authors report. The United States, Germany, Japan, and China accounted for three-quarters of retractions due to fraud or suspected fraud, while China and India accounted for the majority of retractions due to plagiarism and duplicate publication, the study suggests. Retractions due to fraud or error were associated with journals with significantly higher impact factors compared with retractions due to plagiarism and duplicate publication. According to the authors, scientific misconduct appears to have played a more prominent role in retractions in the biomedical literature than previously thought. — S.R.

Unraveling the complications of a biological clock

Pocket chronograph. Image courtesy of Shakko/Wikimedia.

Circadian clocks, which control biological rhythms in tune with daily changes in ambient light and temperature, are composed of proteins called oscillators. Cyanobacterial oscillators consist of three proteins, KaiA, KaiB, and KaiC, whose interactions generate self-sustained 24 h biochemical rhythms. Yong-Gang Chang et al. (pp. 16847–16851) performed a biochemical analysis of the clock proteins of the cyanobacterium Thermosynechococcus elongatus to uncover the molecular workings that drive the oscillator. Though researchers previously showed that the cyanobacterial oscillator can be reconstituted in a test tube by mixing the three proteins in the presence of the chemical compound ATP, the cellular energy currency, the oscillator’s precise mechanism remains elusive. The authors report that rhythmic stacking between two ring-shaped structures called CI and CII, both found in the KaiC protein, propels the oscillator clockwise. In addition, the authors found that ring stacking explains how the chemical compound ADP, a naturally occurring cellular derivative of ATP, can reset the clock. According to the authors, rhythmic ring stacking and unstacking together provide an explanation for circadian clock function, implicated in a range of human diseases. — P.N.

Drug class protects against ALS and Parkinson in mouse, worm models

Prolonged administration of P7C3, a proneurogenic, neuroprotective aminopropyl carbazole, safely restores hippocampal structure and function to mice suffering from pathologically high levels of neuronal apoptosis in the dentate gyrus. Researchers have also known that administering P7C3 to aged rats impedes hippocampal cell death and enhances cognitive ability related to terminal aging. Two studies examine whether the demonstrated action of P7C3 can be extended to models of human degenerative brain disease. Rachel Tesla et al. (pp. 17016–17021) provide evidence that P7C3A20, a highly active analog of P7C3, protects ventral horn spinal cord motor neurons from cell death in a mouse model of amyotrophic lateral sclerosis (ALS). When administered at disease onset, the authors report, reductions in cell death correlated with measurable improvements in motor function decline. In a related study, Héctor De Jesús-Cortés et al. (pp. 17010–17015) found that P7C3 also protects mature neurons in brain regions outside of the hippocampus, and in particular, blocks the death of dopaminergic neurons in the substantia nigra of adult mice, an accepted model of Parkinson disease (PD). The authors show that P7C3 and P7C3A20 protect against the loss of dopaminergic neurons and preserve mobility in a Caenorhabditis elegans PD model, and in addition, demonstrate the hippocampal proneurogenic efficacy of four new P7C3 analogs. These four analogs, the authors report, also protected test subjects in a mouse model of PD. Both studies highlight the specific role of the P7C3 class of drugs by showing that Dimebon, an experimental antihistaminergic treatment with significantly weaker proneurogenic and neuroprotective properties, confers no protection in either the ALS or PD models. Taken together, the findings suggest that the chemical scaffold represented by P7C3 and P7C3A20 may provide a basis to discover and optimize future pharmacologic agents aimed at treating human neurodegenerative diseases such as ALS and PD, according to the authors. — T.J.

Visual neurons acquire selectivity when searching for patterns

Visual cortical neurons respond to certain features of objects, such as color, orientation, and shape. Known as selectivity, this ability to key on specific patterns usually manifests in the initial spike of the neurological response, suggesting that the visual cortex is largely hard-wired for a wide range of stimuli. In Michael Goldberg’s Inaugural Article, Anna Ipata et al. (pp. 16778–16785) show that V4 visual neurons in monkeys develop selectivity for a sought-after pattern when the task requires distinguishing between patterns in the visual field. According to the authors, when test subjects were required to search for a capital “T” among variously oriented lowercase “t” distractors, V4 neurons became selective for the target approximately 40 ms after selectivity appeared for basic pattern features like orientation and color. However, when locating the object in space required simply turning by a specified amount, V4 neurons did not distinguish the search target from the distracters, the authors report. The findings suggest that the brain uses a late-developing selectivity for tasks that require “feature attention” or searching within the receptive field, according to the authors. — T.J.

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