Transport genes and chemotaxis in Laribacter hongkongensis: a genome-wide analysis

Background

Laribacter hongkongensis is a Gram-negative, sea gull-shaped rod associated with community-acquired gastroenteritis. The bacterium has been found in diverse freshwater environments including fish, frogs and drinking water reservoirs. Using the complete genome sequence data of L. hongkongensis, we performed a comprehensive analysis of putative transport-related genes and genes related to chemotaxis, motility and quorum sensing, which may help the bacterium adapt to the changing environments and combat harmful substances.

Results

A genome-wide analysis using Transport Classification Database TCDB, similarity and keyword searches revealed the presence of a large diversity of transporters (n = 457) and genes related to chemotaxis (n = 52) and flagellar biosynthesis (n = 40) in the L. hongkongensis genome. The transporters included those from all seven major transporter categories, which may allow the uptake of essential nutrients or ions, and extrusion of metabolic end products and hazardous substances. L. hongkongensis is unique among closely related members of Neisseriaceae family in possessing higher number of proteins related to transport of ammonium, urea and dicarboxylate, which may reflect the importance of nitrogen and dicarboxylate metabolism in this assacharolytic bacterium. Structural modeling of two C⁴-dicarboxylate transporters showed that they possessed similar structures to the determined structures of other DctP-TRAP transporters, with one having an unusual disulfide bond. Diverse mechanisms for iron transport, including hemin transporters for iron acquisition from host proteins, were also identified. In addition to the chemotaxis and flagella-related genes, the L. hongkongensis genome also contained two copies of qseB/qseC homologues of the AI-3 quorum sensing system.

Conclusions

The large number of diverse transporters and genes involved in chemotaxis, motility and quorum sensing suggested that the bacterium may utilize a complex system to adapt to different environments. Structural modeling will provide useful insights on the transporters in L. hongkongensis.     

A Biochemical Study of Spore Germination in the Blue-green Alga Anabaena doliolum

The spores of Anabaena doliolum formed in light (light spores)and after transfer to darkness (dark spores) are biochemicallydifferent in that the light spores contain chlorophyll a andphycocyanin, while dark spores seem to lack them. The apparentbiosyntheses accompanying dark-spore germination seem to proceedin the following order: RNA, chlorophyll a, phycocyanin andDNA. Results of chloramphenicol treatment indicate that proteinsynthesis precedes RNA synthesis. The biosynthetic events followingRNA synthesis show a requirement for light.     

Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion)

We describe here a case of homologous introns containing homologous open reading frames (ORFs) that are inserted at the same site in the large subunit (LSU) rRNA gene of different organelles in distantly related organisms. We show that the chloroplast LSU rRNA gene of the green alga Chlamydomonas pallidostigmatica contains a group I intron (CpLSU.2) encoding a site-specific endonuclease (I-CpaI). This intron is inserted at the identical site (corresponding to position 1931-1932 of the Escherichia coli 23S rRNA sequence) as a group I intron (AcLSU.m1) in the mitochondrial LSU rRNA gene of the amoeboid protozoon Acanthamoeba castellanii. The CpLSU.2 intron displays a remarkable degree of nucleotide similarity in both primary sequence and secondary structure to the AcLSU.m1 intron; moreover, the Acanthamoeba intron contains an ORF in the same location within its secondary structure as the CpLSU.2 ORF and shares with it a strikingly high level of amino acid similarity (65%; 42% identity). A comprehensive survey of intron distribution at site 1931 of the chloroplast LSU rRNA gene reveals a rather restricted occurrence within the polyphyletic genus Chlamydomonas, with no evidence of this intron among a number of non- Chlamydomonad green algae surveyed, nor in land plants. A parallel survey of homologues of a previously described and similar intron/ORF pair (C. reinhardtii chloroplast CrLSU/A. castellanii mitochondrial AcLSU.m3) also shows a restricted occurrence of this intron (site 2593) among chloroplasts, although the intron distribution is somewhat broader than that observed at site 1931, with site-2593 introns appearing in several green algal branches outside of the Chlamydomonas lineage. The available data, while not definitive, are most consistent with a relatively recent horizontal transfer of both site-1931 and site- 2593 introns (and their contained ORFs) between the chloroplast of a Chlamydomonas-type organism and the mitochondrion of an Acanthamoeba- like organism, probably in the direction chloroplast to mitochondrion. The data also suggest that both introns could have been acquired in a single event.      

The "iatrogenic-hanging columella": preserving columellar contour after tip retroprojection

This article discusses a method for treating the ultraprojecting tip by the resection of columellar skin in open rhinoplasty. Lack of postoperative contraction of columellar skin and soft tissue may result in an "iatrogenic-hanging columella." Columellar skin resection frequently produces its own deformities because of a discrepancy in the width of the columellar base side and the infralobular flap side. The ultraprojecting tip was present in 56 of 660 consecutive rhinoplasty patients (8 percent) over 8 years (1991 to 1998). Of these 56 patients, 48 underwent partial resection of the infralobular skin flap. Of these 48 patients, eight (17 percent) required secondary skin revision of the columellar resection area. The technique was then modified since 1998. Over 2 years, 13 of 129 consecutive rhinoplasty patients (10 percent) were judged to have an ultraprojecting tip. Of these, eight patients were treated with a modification in the technique by resecting skin on the posterior columellar base. No resection areas were revised in the second series. Of the 789 patients in both series, 647 (82 percent) underwent primary rhinoplasties, 126 (16 percent) had secondary rhinoplasties, and 16 (2 percent) had tertiary rhinoplasties. The treatment of excess columella skin adds a subtle aesthetic improvement to the postoperative nasal contour. By resecting skin on the posterior columellar base or the posterior columellar base and, rarely, the anterior flap, an iatrogenic-hanging columella can be avoided.     

Nasal osteotomies: a clinical comparison of the perforating methods versus the continuous technique

Do perforating lateral osteotomies cause less ecchymosis and edema compared with the popular continuous method? Many studies have demonstrated that perforated osteotomies cause less trauma and periosteal disruption. Numerous investigators have subjectively perceived less postoperative ecchymosis and edema, but no clinical study has compared the perforated methods versus the continuous technique in the same patient. This prospective, randomized, partially blinded study was designed to test the hypothesis that the perforating method causes less postoperative ecchymosis and edema compared with the continuous lateral osteotomy technique. The questions remain: does the type of perforating osteotomy affect the results? Does a percutaneous approach cause more ecchymosis and edema by the access maneuver of piercing the skin? The two perforating lateral nasal osteotomy techniques require the same 2-mm straight osteotome, so any genuine difference in postoperative ecchymosis or edema could only be attributed to the differing surgical approaches. Accordingly, this study also tests whether the external percutaneous perforating osteotomy causes more ecchymosis and edema than the internal transnasal perforating method. Twenty-five consecutive rhinoplasty patients (group A) requiring bilateral osteotomies (50 total lateral osteotomies) were randomized so that each patient received an internal/transnasal perforating lateral osteotomy (2-mm straight chisel) on one side and an internal/transnasal continuous osteotomy (4-mm curved, guarded osteotome) on the other. The next 25 patients studied (group B) received an external/percutaneous perforating lateral osteotomy (same 2-mm straight chisel as used in group A) on one side and the same internal/transnasal continuous osteotomy on the other. The final 25 consecutive rhinoplasty patients (group C) received an external percutaneous perforating lateral osteotomy on one side and an internal transnasal perforating lateral osteotomy on the other. The entry sites for the perforating osteotomies were either external (groups B and C) with a percutaneous skin puncture or intranasal (groups A and C) at the pyriform aperture. All 75 patients (150 total lateral osteotomies) initialed the surgical plan on the Gunter rhinoplasty worksheet, which has been approved by the Institutional Review Board of Abbott-Northwestern Hospital, Minneapolis, Minnesota (study no. 1341-1 M). All patients were evaluated for ecchymosis and edema on the left versus the right side of the face at 2 to 3, 7, and 21 days after the operation. The clinical evaluation was performed by two blinded examiners (clinic registered nurse and the patient with his or her family) and a partially blinded examiner (the surgeon, who did not refresh his memory about the randomization). To compare the two methods in each study (groups A, B, and C) for the six outcomes (edema and ecchymosis at 2 to 3, 7, and 21 days), the authors used an exact binomial test of the null hypothesis that the treatments do not differ. To compare the two methods in each study (groups A, B, and C) using all six outcomes simultaneously, the authors used a permutation test. By both testing methods, the perforating internal method was superior to the continuous technique (group A; p < 0.01 in both tests). Although the perforating external method gave better results than the continuous technique (group B) and the perforating internal method gave better results than the perforating external method (group C), neither of these differences was significant by either testing method. A lateral osteotomy technique should be precise, reproducible, and safe, and it should minimize ecchymosis and edema. Since edema and ecchymosis are comparable regardless of osteotome size, this prospective randomized study confirms the subjective clinical impression that perforating lateral osteotomies with a 2-mm straight osteotome reduce postoperative ecchymosis and edema in rhinoplasty patients compared with the continuous osteotomy (4-mm curved, guarded osteotome). These findings should encourage te the use of perforating osteotomies rather than continuous osteotomies.     

The use of alloderm for the correction of nasal contour deformities

What rhinoplasty surgeon has not been frustrated by unmet expectations from unreliable graft materials? The quest for an ideal graft continues. Septal cartilage is not always adequate in amount or substance. Ear cartilage may cause unsightly irregularities over time. Cranial bone or rib harvest sites add to the complexity of the procedure and can be intimidating for many operators. This article describes the authors' successful experience with AlloDerm onlay grafts for the correction of nasal contour deformities in 58 primary and secondary rhinoplasty cases by means of the open and endonasal approaches. Forty-two patients received an open-approach procedure; the remaining 16 received grafting through an endonasal or closed approach. Thirty-seven of the patients were secondary rhinoplasty patients, and some underwent multiple nasal corrections. The indications, intraoperative surgical technique of graft placement, and representative results will be discussed. Long-term follow-up showed good results, though partial graft resorption occurred in some patients. Overall, this experience with AlloDerm for nasal augmentation was encouraging.     

Medaka fish exhibits longevity gender gap,a natural drop in estrogen and telomere shortening during aging: a unique model for studying sex-dependent longevity

Introduction

Females having a longer telomere and lifespan than males have been documented in many animals. Such linkage however has never been reported in fish. Progressive shortening of telomere length is an important aging mechanism. Mounting in vitro evidence has shown that telomere shortening beyond a critical length triggered replicative senescence or cell death. Estrogen has been postulated as a key factor contributing to maintenance of telomere and sex-dependent longevity in animals. This postulation remains unproven due to the lack of a suitable animal system for testing. Here, we introduce a teleost model, the Japanese medaka Oryzias latipes, which shows promise for research into the molecular mechanism(s) controlling sex difference in aging.

Results

Using the medaka, we demonstrate for the first time in teleost that (i) sex differences (female?>?male) in telomere length and longevity also exist in fish, and (ii) a natural, ‘menopause’-like decline of plasma estrogen was evident in females during aging. Estrogen levels significantly correlated with telomerase activity as well as telomere length in female organs (not in males), suggesting estrogen could modulate telomere length via telomerase activation in a sex -specific manner. A hypothetical in vivo ‘critical’ terminal restriction fragment (TRF, representing telomere) length of approximately 4 kb was deduced in medaka liver for prediction of organismal mortality, which is highly comparable with that for human cells. An age conversion model was also established to enable age translation between medaka (in months) and human (in years). These novel tools are useful for future research on comparative biology of aging using medaka.

Conclusion

The striking similarity in estrogen profile between aging female O. latipes and women enables studying the influence of “postmenopausal” decline of estrogen on telomere and longevity without the need of invasive ovariectomy. Medaka fish is advantageous for studying the direct effect of increased estrogen on telomere length and longevity without the breast cancer complications reported in rodents. The findings strongly support the notion that O. latipes is a unique non-mammalian model for validation of estrogenic influence on telomere and longevity in vertebrates. This laboratory model fish is of potential significance for deciphering the ostensibly conserved mechanism(s) of sex-associated longevity in vertebrates.

     

Chemical biology: Paper alert

A selection of interesting papers that were published in the two months before our press date in major journals most likely to report significant results in chemical biology.