Cellular nucleic acid binding protein binds G-rich single-stranded nucleic acids and may function as a nucleic acid chaperone

Cellular nucleic acid binding protein (CNBP) is a small single-stranded nucleic acid binding protein made of seven Zn knuckles and an Arg-Gly rich box. CNBP is strikingly conserved among vertebrates and was reported to play broad-spectrum functions in eukaryotic cells biology. Neither its biological function nor its mechanisms of action were elucidated yet. The main goal of this work was to gain further insights into the CNBP biochemical and molecular features. We studied Bufo arenarum CNBP (bCNBP) binding to single-stranded nucleic acid probes representing the main reported CNBP putative targets. We report that, although bCNBP is able to bind RNA and single-stranded DNA (ssDNA) probes in vitro, it binds RNA as a preformed dimer whereas both monomer and dimer are able to bind to ssDNA. A systematic analysis of variant probes shows that the preferred bCNBP targets contain unpaired guanosine-rich stretches. These data expand the knowledge about CNBP binding stoichiometry and begins to dissect the main features of CNBP nucleic acid targets. Besides, we show that bCNBP presents a highly disordered predicted structure and promotes the annealing and melting of nucleic acids in vitro. These features are typical of proteins that function as nucleic acid chaperones. Based on these data, we propose that CNBP may function as a nucleic acid chaperone through binding, remodeling, and stabilizing nucleic acids secondary structures. This novel CNBP biochemical activity broadens the field of study about its biological function and may be the basis to understand the diverse ways in which CNBP controls gene expression.     

Modulation of physiological performance by temperature and salinity in the sugar kelp Saccharina latissima

The sugar kelp Saccharina latissima experiences a wide range of environmental conditions along its geographical and vertical distribution range. Temperature and salinity are two critical drivers influencing growth, photosynthesis and biochemical composition. Moreover, interactive effects might modify the results described for single effects. In shallow water coastal systems, exposure to rising temperatures and low salinity are expected as consequence of global warming, increased precipitation and coastal run‐off. To understand the acclimation mechanisms of S. latissima to changes in temperature and salinity and their interactions, we performed a mechanistic laboratory experiment in which juvenile sporophytes from Brittany, France were exposed to a combination of three temperatures (0, 8 and 15°C) and two salinity levels (20 and 30 psu (practical salinity units)). After a temperature acclimation of 7 days, sporophytes were exposed to low salinity (20 psu) for a period of 11 days. Growth, and maximal quantum yield of photosystem II (Fv/Fm), pigments, mannitol content and C:N ratio were measured over time. We report for the first time in S. latissima a fivefold increase in the osmolyte mannitol in response to low temperature (0°C) compared to 8 and 15°C that may have ecological and economic implications. Low temperatures significantly affected all parameters, mostly in a negative way. Chlorophyll a, the accessory pigment pool, growth and Fv/Fm were significantly lower at 0°C, while the de‐epoxidation state of the xanthophyll cycle was increased at both 0 and 8°C compared to 15°C. Mannitol content and growth decreased with decreased salinity; in contrast, pigment content and Fv/Fm were to a large extent irresponsive to salinity. In comparison to S. latissima originating from an Arctic population, despite some reported differences, this study reveals a remarkably similar impact of temperature and salinity variation, reflecting the large degree of adaptability in this species.     

Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils

To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1–2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.     

Addiction: Decreased reward sensitivity and increased expectation sensitivity conspire to overwhelm the brain's control circuit

Based on brain imaging findings, we present a model according to which addiction emerges as an imbalance in the information processing and integration among various brain circuits and functions. The dysfunctions reflect (a) decreased sensitivity of reward circuits, (b) enhanced sensitivity of memory circuits to conditioned expectations to drugs and drug cues, stress reactivity, and (c) negative mood, and a weakened control circuit. Although initial experimentation with a drug of abuse is largely a voluntary behavior, continued drug use can eventually impair neuronal circuits in the brain that are involved in free will, turning drug use into an automatic compulsive behavior. The ability of addictive drugs to co‐opt neurotransmitter signals between neurons (including dopamine, glutamate, and GABA) modifies the function of different neuronal circuits, which begin to falter at different stages of an addiction trajectory. Upon exposure to the drug, drug cues or stress this results in unrestrained hyperactivation of the motivation/drive circuit that results in the compulsive drug intake that characterizes addiction.     

Alleles on Rat Chromosome 4 (D4Got41‐Fabp1/Tacr1) Regulate Subphenotypes of Obesity

Objective: The use of inbred animal models is an essential component of the genetic dissection of complex diseases. Because quantitative trait loci for serum triglycerides, total cholesterol, and body weight were mapped on chromosome 4 in a cross of BioBreeding/OttawaKarlsburg (BB/OK) and spontaneously hypertensive (SHR) rats, we established a congenic BB.SHR rat strain by introgressing a SHR segment of chromosome 4 (D4Got41‐Tacr1) into a BB/OK background. The phenotype of these BB.SHR rats (BB.4S) confirmed the quantitative trait loci. To discover whether the phenotype of BB.4S can only be attributed to the SHR segment per se, we established an additional congenic BB.WOKW strain by introgressing a similar segment of chromosome 4 (D4Got41‐Fabp1) of the Wistar Ottawa Karlsburg RT1^u rat into a BB/OK background, termed briefly BB.4W. Research Methods and Procedures: Male normoglycemic BB/OK (20), BB.4S (20), and BB.4W (16) rats were longitudinally studied for body weight, serum triglycerides, total and high‐density lipoprotein‐cholesterol, and glucose tolerance. At the end of the observation period (32 weeks), serum insulin, leptin, and adiposity index (AI) were determined. Results and Discussion: Congenic BB.4S and BB.4W were significantly heavier, and AI, serum triglycerides, and total cholesterol values were significantly elevated in BB.4S and BB.4W compared with BB/OK but more pronounced in BB.4S. The highest serum insulin was found in BB.4W and highest leptin in BB.4S. Because the body weight gain and AI were comparable between BB.4S and BB.4W, the obviously higher insulin levels in BB.4W and higher leptin values in BB.4S suggest that the two congenics most probably define two subphenotypes of obesity and provide the unique opportunity to study their genetics.     

Systematic analysis of ATG13 domain requirements for autophagy induction

Macroautophagy/autophagy is an evolutionarily conserved cellular process whose induction is regulated by the ULK1 protein kinase complex. The subunit ATG13 functions as an adaptor protein by recruiting ULK1, RB1CC1 and ATG101 to a core ULK1 complex. Furthermore, ATG13 directly binds both phospholipids and members of the Atg8 family. The central involvement of ATG13 in complex formation makes it an attractive target for autophagy regulation. Here, we analyzed known interactions of ATG13 with proteins and lipids for their potential modulation of ULK1 complex formation and autophagy induction. Targeting the ATG101-ATG13 interaction showed the strongest autophagy-inhibitory effect, whereas the inhibition of binding to ULK1 or RB1CC1 had only minor effects, emphasizing that mutations interfering with ULK1 complex assembly do not necessarily result in a blockade of autophagy. Furthermore, inhibition of ATG13 binding to phospholipids or Atg8 proteins had only mild effects on autophagy. Generally, the observed phenotypes were more severe when autophagy was induced by MTORC1/2 inhibition compared to amino acid starvation. Collectively, these data establish the interaction between ATG13 and ATG101 as a promising target in disease-settings where the inhibition of autophagy is desired.     

Aerobic biodegradation of a mixture of sulfonated azo dyes by a bacterial consortium immobilized in a two‐stage sparged packed‐bed biofilm reactor

The biodegradation of the sulfonated azo dyes, Acid Orange 7 (AO7) and Acid Red 88 (AR88), by a bacterial consortium isolated from water and soil samples obtained from sites receiving discharges from textile industries, was evaluated. For a better removal of azo dyes and their biodegradation byproducts, an aerobically operated two‐stage rectangular packed‐bed biofilm reactor (2S‐RPBR) was constructed. Because the consortium's metabolic activity is affected by oxygen, the effect of the interstitial air flow rate Q_GI on 2S‐RPBR's zonal values of the oxygen mass transfer coefficient k_La was estimated. In the operational conditions probed in the bioreactor, the k_La values varied from 3 to 60 h^?1, which roughly correspond to volumetric oxygen transfer rates, dc_L/dt, ranging from 20 to 375 mg O₂ L^?1h^?1. Complete biodegradation of azo dyes was attained at loading rates B_V,AZ up to 40 mg L^?1d^?1. At higher B_V,AZ values (80 mg L^?1 d^?1), dye decolorization and biodegradation of the intermediaries 4‐amino‐naphthalenesulphonic acid (4‐ANS) and 1‐amino‐2‐naphthol (1‐A2N) was almost complete. However, a diminution in COD and TOC removal efficiencies was observed in correspondence to the 4‐aminobenzenesulfonic acid (4‐ABS) accumulation in the bioreactor. Although the oxygen transport rate improved the azo dye mineralization, the results suggest that the removal efficiency of azo dyes was affected by biofilm detachment at relatively high Q_GI and B_V,AZ values. After 225 days of continuous operation of the 2S‐RFBR, eight bacterial strains were isolated from the biofilm attached to the porous support. The identified genera were: Arthrobacter, Variovorax, Agrococcus, Sphingomonas, Sphingopyxis, Methylobacterium, Mesorhizobium, and Microbacterium.     

Age–period–cohort analysis of colorectal cancer in East Anglia, 1971–2005

Background: This study aimed to investigate the incidence trends of colorectal cancer by sex and subsite, in East Anglia from 1971 to 2005. Methods: Using data from the Eastern Cancer Registration and Information Centre, we examined the time trends and the effect of age, period of diagnosis and birth cohort on the incidence of colorectal cancer by sex and subsite. Results: Between 1971 and 2005, 23 875 males and 22 651 females were registered with colorectal cancer in East Anglia. During this period, the increase in the incidence trends was higher among males, more recent periods of diagnosis, and proximal colon. Cohort effects were statistically significant in distal and rectal cancers in males (p < 0.001 and p = 0.05, respectively), and in proximal colon in females (p < 0.001). Period effects were statistically significant across all subsites and both sexes (p < 0.001 for all). Conclusions: Period effects were significant across all subsites for both sexes, whereas cohort effects varied in their significance levels depending on subsite and sex. We suggest that the period effect may be due to an increase in the use of colonoscopy for diagnostic or opportunistic screening, and the cohort effect may be due to aetiological differences in CRC between sexes and subsites.     

Genome Sequence of Streptococcus gallolyticus: Insights into Its Adaptation to the Bovine Rumen and Its Ability To Cause Endocarditis

Streptococcus gallolyticus (formerly known as Streptococcus bovis biotype I) is an increasing cause of endocarditis among streptococci and frequently associated with colon cancer. S. gallolyticus is part of the rumen flora but also a cause of disease in ruminants as well as in birds. Here we report the complete nucleotide sequence of strain UCN34, responsible for endocarditis in a patient also suffering from colon cancer. Analysis of the 2,239 proteins encoded by its 2,350-kb-long genome revealed unique features among streptococci, probably related to its adaptation to the rumen environment and its capacity to cause endocarditis. S. gallolyticus has the capacity to use a broad range of carbohydrates of plant origin, in particular to degrade polysaccharides derived from the plant cell wall. Its genome encodes a large repertoire of transporters and catalytic activities, like tannase, phenolic compounds decarboxylase, and bile salt hydrolase, that should contribute to the detoxification of the gut environment. Furthermore, S. gallolyticus synthesizes all 20 amino acids and more vitamins than any other sequenced Streptococcus species. Many of the genes encoding these specific functions were likely acquired by lateral gene transfer from other bacterial species present in the rumen. The surface properties of strain UCN34 may also contribute to its virulence. A polysaccharide capsule might be implicated in resistance to innate immunity defenses, and glucan mucopolysaccharides, three types of pili, and collagen binding proteins may play a role in adhesion to tissues in the course of endocarditis.Several studies have reported that the proportion of infective endocarditis due to Streptococcus gallolyticus has increased during the last decades, concomitantly with a decrease of cases due to oral streptococci (35). S. gallolyticus is now becoming the first cause of infectious endocarditis among streptococci in Europe (16). Furthermore, S. gallolyticus endocarditis is associated with rural residency, suggesting transmission from animals (29). However, the reasons for the emergence of this pathogen remain poorly understood. S. gallolyticus belongs to the Streptococcus bovis group known for more than 60 years to cause endocarditis (45). Recently, the former species S. bovis has been divided into four major species (50, 53). S. gallolyticus corresponds to S. bovis biotype I (mannitol fermentation positive), the closely related species S. pasteurianus to biotype II/2 (mannitol negative and β-glucuronidase positive), and the more distantly related species S. infantarius to biotype II/1 (mannitol negative and β-glucuronidase negative). S. macedonicus, the fourth species, commonly found in cheese, is nonpathogenic and also considered a S. gallolyticus subspecies (53, 62). A majority of endocarditis cases was due, among the formerly S. bovis group, to S. gallolyticus strains (4).Multiple studies have shown that endocarditis due to S. gallolyticus as well as positive blood culture for this species is often associated with gastrointestinal malignancy (4, 6). This association has led to a strong indication for gastrointestinal investigation and endoscopic follow-up in the case of S. gallolyticus infections (66). The association of S. gallolyticus infection with colon cancer is a major but still unsolved issue. It may be just incidental, as the alteration of the digestive mucosa may favor the translocation of the bacteria into the bloodstream. Alternatively, the tumor may contribute to the proliferation of S. gallolyticus in close proximity to the gut epithelium, increasing its probability of translocating through the gut barrier. It has also been suggested that the bacterium itself contributes to carcinogenesis (60, 69). In addition to human disease, S. gallolyticus may also cause diseases in animals, like septicemia in pigeons (19), outbreaks in broiler flocks (11), or bovine mastitis (28).Independent from its association to disease, S. gallolyticus has been isolated as a tannin-resistant bacterium from the feces of different mammalian herbivores, including the koala (48) or the Japanese large wood mouse (52), and it is also a normal inhabitant of the rumen (39). Its resistance to tannins is linked to its tannase activity, a characteristic which also led this bacterium to be named “gallolyticus” as it is able to decarboxylate gallate, an organic acid derived from tannin degradation. S. gallolyticus is also known to express other degradative functions unique among streptococci, like a bile salt hydrolase or an amylase. These properties allow its multiplication outside the animal host, as S. gallolyticus was isolated from a digester fed with shea cake (derived from the nuts of the African tree Vitellaria paradoxa) rich in tannins and aromatic compounds (12). S. gallolyticus is a commensal of the human intestinal tract but remains a rarely detected (2.5 to 15%) low-abundance species (10, 40). In herbivores, overgrowth of S. bovis may become deleterious. For example, ingestion of large amounts of rapidly fermented cereal grains leads to a destabilization of the rumen flora and to the proliferation of acid-tolerant bacteria, including S. gallolyticus. This is accompanied by the overproduction of mucopolysaccharides that stabilize the foam, resulting in feedlot bloat, a significant cause of economical loss (14).Virulence and colonization factors of S. gallolyticus in humans are largely unknown. Studies of the bird host have shown that this Streptococcus species expresses a capsular polysaccharide, and five different serotypes have been described (19). In addition, electron microscopy studies have revealed the presence of fimbria-like structures on the surface of S. gallolyticus. It was hypothesized that capsules and/or fimbriae are involved in virulence (63). S. gallolyticus isolates responsible for endocarditis exhibited heterogeneous patterns of adherence to extracellular matrix (ECM) proteins, which suggests that they produce different surface components (55). Recently, a collagen binding adhesin together with 10 putative ECM binding proteins were identified in the draft genome sequence of a human isolate of S. gallolyticus (54).Here we describe the sequence and analysis of the genome of S. gallolyticus strain UCN34 isolated from a human case of endocarditis associated with colon cancer. Analysis of the predicted proteins revealed unique metabolic and cell surface features among streptococci, which contribute to its adaptation to the rumen and to its ability to cause endocarditis. We showed by comparative genomics that many of the corresponding genes were probably acquired by lateral gene transfer (LGT) from other Firmicutes of the gut microbiota.