The origin of a novel gene through overprinting in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Background  

Overlapped genes originate by a) loss of a stop codon among contiguous genes coded in different frames; b) shift to an upstream initiation codon of one of the contiguous genes; or c) by overprinting, whereby a novel open reading frame originates through point mutation inside an existing gene. Although overlapped genes are common in viruses, it is not clear whether overprinting has led to new genes in prokaryotes.     

Rapid enhancement of biodiversity occurrence records using unconventional specimen data

Distributions of taxa across time and space are central to understanding biodiversity and biotic change, yet currently available occurrence data, drawn from biodiversity specimen records and observational datasets, are often insufficient to answer many driving questions. Records of “associated taxa,” taxa co-occurring with a specimen at the time and place of collection, have the potential to fill data gaps and expand the spatiotemporal scope of current occurrence records. I developed a method to extract associated taxon records from 84,328 digitized specimen records and examined the potential of these data to improve the quantity and quality of existing species occurrence data. Adding associated taxon records increased the size of the test dataset by 18.5%, spanned multiple decades (1937–2016), and potentially extended the known range of 217 taxa in Florida and up to 1500 taxa in the United States, demonstrating the capacity of these records to deepen our understanding of changes in the distributions of taxa on Earth. These results suggest that increased attention to documenting associated taxa could be a promising way to maximize the impact of every collecting event.     

Roles of Peroxisome Proliferator-Activated Receptor Gamma on Brain and Peripheral Inflammation

Peroxisome proliferator-activated receptor gamma (PPARγ) has been implicated in the pathology of numerous diseases involving diabetes, stroke, cancer, or obesity. It is expressed in diverse cell types, including vessels, immune and glial cells, and neurons. PPARγ plays crucial roles in the regulation of cellular differentiation, lipid metabolism, or glucose homeostasis. PPARγ ligands also exert effects on attenuating degenerative processes in the brain, as well as in peripheral systems, and it has been associated with the control of anti-inflammatory mechanisms, oxidative stress, neuronal death, neurogenesis, differentiation, and angiogenesis. This review will highlight key advances in the understanding of the PPARγ-related mechanisms responsible for neuroprotection after brain injuries, both ischemia and traumatic brain injury, and it will also cover the natural and synthetic agonist for PPARγ, angiotensin receptor blockers, and PPARγ antagonists, used in experimental and clinical research. A better understanding of the pleiotropic mechanisms and applications of these drugs to improve the recovery and to repair the acute and chronic induced neuroinflammation after brain injuries will pave the way for more effective therapeutic strategies after brain deficits.     

Chromatin in diapause of the silkworm <Emphasis Type="Italic">Bombyx mori</Emphasis> L.: Thermal parthenogenesis and normal development

By using hematoxylin staining, peculiarities of chromatin of diapausing silkworm embryos were studied in normal and parthenogenetic development. A direct correlation was revealed between the number of interphase chromatin grains and the number of chromosomes in the nucleus; polyploidization of cells in embryo was studied at the stage of diapause. The polyploidization in parthenogenesis is not restricted to endomitotic chromosome set doubling, as it includes 6n-nuclei. To explain the more diverse spectrum of polyploid cells in parthenogenesis (as compared with the norm), it is necessary to take into account fusion of cleavage nuclei, which is realized by the cytoplasmic mechanism of karyogamy in the absence of fertilization. On squash preparations, for the first time, we identified primordial germ cells of the diapausing embryo, which are characterized by less compact chromatin, especially in the zygotic variant of development; by larger nuclei and cytoplasm; and by an irregular number and size of nucleoli. Estimation of ploidy of the primary germ cells in parthenogenesis by counting “loose” chromatin grains in diapause is possible and indicates polyploidization in the primordial germ cells. This explains an inevitable admixture of tetraploid eggs in the grain of diploid parthenoclones and its absence in normal development. The cytological method used has revealed a spiral arrangement of chromatin grains on the internal nuclear surface at different ploidy levels.     

Recovery rates of chlorophyll-fluorescence parameters in desiccation-tolerant plants: fitted logistic curves as a versatile and robust source of comparative data

Desiccation-tolerant plants vary greatly in the rate of recovery of chlorophyll-fluorescence parameters on re-wetting. This paper seeks general curves that will adequately describe the course of recovery, and quantify the variations in rate within and between species. Recovery of F _v /F _m is closely fitted in many species by a logistic curve, starting from zero, on a logarithmic time-scale (seconds to days). Such curves have three parameters, an asymptote at maximum F _v /F _m, a half-recovery time (T _0.5), and a slope constant (S). If F _v /F _m in dry material differs substantially from zero, four-parameter logistic curves can give a better fit. In either case, T _0.5 and S show wide ecologically-significant variation. Some species show anomalously high values of F _v /F _m in the early minutes of recovery, alongside low absolute values of F _m; these invite further investigation. Logistic curves give good fits to the recovery in light of Φ _PSII, q _P, and photosynthetic CO₂ fixation. The results provide the means to quantify ‘high-inertia’ versus ‘low-inertia’ strategies of desiccation tolerance, and to explore the factors influencing recovery time and rate, and the reasons for some discrepancies from the common course of recovery. There is substantial overlap in all parameters between the bryophytes and pteridophytes studied.     

Parallel evolution of character displacement driven by competitive selection in terrestrial salamanders

Background  

Parallel evolution can occur when common environmental factors exert similar selective forces on morphological variation in populations in different geographic localities. Competition can also generate morphological shifts, and if competing species co-occur in multiple geographic regions, then repeated instances of competitively-driven morphological divergence (character displacement) can occur. Despite the importance of character displacement for inferring the role of selection in morphological evolution however, replicated instances of sympatric morphological divergence are understudied.     

The development of policy approaches for reducing nitrogen pollution to coastal waters of the USA

Two-thirds of the coastal rivers and bays in the United States are degraded from nutrient pollution, and nitrogen inputs these waters continue to increase. The nitrogen comes from a variety of sources, including runoff from agricultural fields, concentrated animal feeding operations, atmospheric deposition from fossil fuel combustion, and sewage and septic wastes. Technical solutions for nitrogen pollution exist at reasonable cost. That most of these solutions have not yet been implemented to any significant extent across the United States suggests that new policy approaches are necessary. The best solution may involve a combination of voluntary and mandatory approaches, applying different approaches to different sources of nitrogen pollution. A watershed-based approach that relies heavily on voluntary mechanisms (such as crop-yield insurance to reduce over-fertilization) is likely to be the most effective for some sources of nitrogen (such as runoff from agricultural fields), while a uniform national regulatory approach may be better for others (such as NO_x emissions from fossil fuel combustion). Implementation of management strategies should be carefully coupled to monitoring programs to assess the effectiveness of these strategies. While both nitrogen and phosphorus are important to control, the focus should be on nitrogen management, in part because nitrogen is more generally the causal agent of coastal eutrophication. Also, while nitrogen-control practices tend to also reduce phosphorus pollution, phosphorus-control practices often have little effect on nitrogen. Although current scientific and technical knowledge is sufficient to begin to make substantial progress toward solving coastal nitrogen pollution, progress will be made more quickly and more cost effectively with increased investment in appropriate scientific research.     

Lectin Binding Assays for In-Process Monitoring of Sialylation in Protein Production

Many therapeutic proteins require appropriate glycosylation for their biological activities and plasma half life. Coagulation factor VIII (FVIII) is a glycoprotein which has extensive post-translational modification by N-linked glycosylation. The terminal sialic acid in the N-linked glycans of FVIII is required for maximal circulatory half life. The extent of FVIII sialylation can be determined by high pH anion-exchange chromatography coupled with a pulse electrochemical detector (HPAEC-PED), but this requires a large amount of purified protein. Using FVIII as a model, the objective of the present study was to develop assays that enable detection and prediction of sialylation deficiency at an early stage in the process and thus prevent downstream product quality excursions. Lectin ECA (Erythrina Cristagalli) binds to unsialylated Galβ1-4 GlcNAc and the ECA-binding level (i.e., terminal Gal(β1-4) exposure) is inversely proportional to the level of sialylation. By using ECA, a cell-based assay was developed to measure the global sialylation profile in FVIII producing cells. To examine the Galβ1-4 exposure on the FVIII molecule in bioreactor tissue culture fluid (TCF), an ELISA-based ECA-FVIII binding assay was developed. The ECA-binding specificity in both assays was assessed by ECA-specific sugar inhibitors and neuraminidase digestion. The ECA-binding specificity was also independently confirmed by a ST3GAL4 siRNA knockdown experiment. To establish the correlation between Galβ1-4 exposure and the HPAEC-PED determined FVIII sialylation value, the FVIII containing bioreactor TCF and the purified FVIII samples were tested with ECA ELISA binding assay. The results indicated an inverse correlation between ECA binding and the corresponding HPAEC-PED sialylation value. The ECA-binding assays are cost effective and can be rapidly performed, thereby making them effective for in-process monitoring of protein sialylation.     

Genomic information infrastructure after the deluge

Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.