[Mechanical circulatory support combined with immunomodulation treatment for patients with fulminant myocarditis: a single-center real-world study].

Objective: To investigate the relationship between the mechanical circulatory support (MCS) combined with immunomodulation and the prognosis of patients with fulminant myocarditis. Methods: This is a retrospective study. A total of 88 patients with fulminant myocarditis admitted to Dongguan Kanghua hospital from Aug. 2008 to Dec. 2020 were included. Medical histories, results of laboratory tests, treatment regimens and clinical outcomes of these patients during their hospitalization were collected from the medical record system. According to the treatment methods, the patients were divided into MCS+immunomodulation group (38 cases), MCS group (20 cases) and traditional treatment group (30 cases). Patients in the MCS+immunomodulation group received intra-aortic balloon pump (IABP) or IABP combined with extracorporeal membrane oxygenation (ECMO) and immunoglobulin or glucocorticoid. Patients in the MCS group only received mechanical circulatory support. Patients in the traditional treatment group received neither mechanical circulatory support nor immunomodulatory therapy, and only used vasoactive drugs and cardiotonic drugs. The in-hospital mortality and length of stay were compared among the three groups. Results: A total of 88 patients with fulminant myocarditis aged (35.0±10.8) years were included, and there were 46 males (52.3%). The mortality of MCS+immunomodulation group (7.9% (3/38) vs. 56.7% (17/30), P=0.001 2) and MCS group (30.0% (6/20) vs. 56.7% (17/30), P=0.002 8) were lower than that of traditional treatment group. Compared with the MCS group, the in-hospital mortality in the MCS+immunomodulation group was lower (P=0.005 4). The most common cause of death was multiple organ dysfunction syndrome (MODS). The constituent ratios of death in MCS+immunomodulation group, MCS group and traditional treatment group were 3/3, 4/6 and 12/17, respectively. The incidence of MODS in the MCS group (20% (4/20)) and the traditional treatment group (40% (12/30)) was significantly higher than that in the MCS+immunomodulation group (7.9% (3/38)) (both P<0.01). In discharged patients, the hospitalization time of MCS+immunomodulation group was shorter than that of traditional treatment group ((13.4±5.5)d vs. (18.5±7.4)d, P<0.05) and MCS group ((13.4±5.5)d vs. (16.9±8.5)d, P<0.05). Conclusion: MCS combined with immunomodulatory therapy is associated with lower in-hospital mortality and shorter hospital stay in patients with fulminant myocarditis.

Overexpression of miR-101-2 in donor cells improves the early development of Holstein cow somatic cell nuclear transfer embryos.

Accumulating studies have suggested that microRNA play a part in regulating multiple cellular processes, such as cell proliferation, apoptosis, the cell cycle, and embryo development. This study explored the effects of miR-101-2 on donor cell physiological status and the development of Holstein cow somatic cell nuclear transfer (SCNT) embryos in vitro. Holstein cow bovine fetal fibroblasts (BFF) overexpressing miR-101-2 were used as donor cells to perform SCNT; then, cleavage rate, blastocyst rate, inner cell mass-to-trophectoderm ratio, and the expression of some development- and apoptosis-related genes in different groups were analyzed. The miR-101-2 suppressed the expression of inhibitor of growth protein 3 (ING3) at mRNA and protein levels, expedited cell proliferation, and decreased apoptosis in BFF, suggesting that ING3, a target gene of miR-101-2, is a potential player in this process. Moreover, by utilizing donor cells overexpressing miR-101-2, the development of bovine SCNT embryos in vitro was significantly enhanced; the apoptotic rate in SCNT blastocysts was reduced, and the inner cell mass-to-trophectoderm ratio and SOX2, POU5F1, and BCL2L1 expression significantly increased, whereas BAX and ING3 expression decreased. Collectively, these findings suggest that miR-101-2 promotes BFF proliferation and vitality, reduces their apoptosis, and improves the early development of SCNT embryos.

[Molecular detection and genotyping of human papillomavirus].

The development of cervical cancer is associated with persistent infection of high-risk human papillomavirus. The detection and genotyping of HPV could be used to evaluate the epidemiology of HPV infections, monitor HPV vaccine efficacy, and screen cervical cancer. There are a lot of commercially available molecular tests for HPV, based on different methodologies and detection systems. In principle, it mainly includes two categories, namely signal amplification and target amplification. Most of them are based on PCR amplification, such as fluorescent PCR, PCR-reverse hybridization, etc. The performances of detection reagents are different. In addition, HPV genotyping assays based on next-generation sequencing and quantitative HPV detection kits are developed. However, only a small number of commercial assays have been clinically verified. A large number of assays which may bring greater values in the screening of cervical cancer are needed to be clinically validated.

[Establishment and evaluation of a new method for determining hemodynamics of pulmonary hypertension rats].

Objective: By evaluating the hemodynamic parameters such as cardiac output (CO), right ventricular pressure (RVP), pulmonary artery pressure (PAP) and total pulmonary resistance index (TPRI) in pulmonary hypertension rat model, we established a more comprehensive hemodynamic evaluation system, which objectively evaluated the severity of disease and exercise tolerance in rats with pulmonary hypertension. Methods: SD rats were randomly divided into a control group and a model group with 5 rats in each group. The model group was intraperitoneally injected with SU5416 (20 mg/kg) and placed in an oxygen chamber at a 10% oxygen concentration for 21 days and then placed in a normoxic environment for 14 days. After modeling, rats were anesthetized and mechanically ventilated. The operator cut the skin along the right paraxial line, detached and ligated the intercostal artery, and then cut off the 3 and 4 ribs, exposing the heart and freeing aortic root about 0.2 cm. The flowmeter probe was set in the dissected aortic segment, and real-time recording time, blood flow waveforms, cardiac output were calculated accordingly. Then the needle attached to the baroreceptor was inserted into the right ventricle and the system acquired the right ventricular time-pressure waveform. After the waveform stabilized for about 30 seconds, the end of the cannula was sent to the pulmonary artery trunk through the entrance of the pulmonary artery to record the time-pressure curve of the pulmonary artery. Results: RVSP, PASP, PADP and mPAP in the model group were significantly higher than those of the control group [ RVSP(23.4±5.4) mmHg, 1 mmHg=0.133 kPa vs (56.4±13.0) mmHg, PASP (22.8±4.4) mmHg vs (58.5±14.9) mmHg, PADP (9.7±1.9) mmHg vs (30.3±7.0) mmHg, mPAP (14.1±2.7) mmHg vs (41.9±8.0) mmHg, all P<0.05 ]. Compared with the control group, the cardiac index in the model group was significantly lower [ CI (0.54±0.08) ml·min(-1)·g(-1) vs (0.40±0.09) ml·min(-1)·g(-1,) P=0.02 ]. Furthermore, compared with the control group, pulmonary vascular resistance index was significantly increased in the model group[PVRI (0.27±0.03) mmHg·ml(-1)·min(-1)·kg(-1) vs (0.06±0.01) mmHg·ml(-1)·min(-1)·kg(-1,) P<0.05]. The pathological results also showed that the middle part of pulmonary arterioles in the model group had muscular hypertrophy and muscular pulmonary arterioles, and even plexiform lesions. Conclusion: In this study, we established a new method that simultaneously determined several hemodynamic parameters such as RVSP, PASP, PADP, CO, CI and PVRI, which provided a more comprehensive assessment of hemodynamic changes in pulmonary hypertension rat models.

[Primary culture and functional identification of distal pulmonary artery smooth muscle cells in mice].

Objective: To establish a method of isolation and primary culture of mice distal pulmonary artery smooth muscle cells (PASMCs) and identify the functional properties. Methods: PASMCs were harvested from the distal pulmonary artery (PA) tissue of mice by enzymatic digestion of collagenaseⅠand papain; and the growth characteristics were observed under inverted microscope and identified by Immunofluorescence technique. Effects on the intracellular calcium ion concentration of distal PASMCs were detected by Fura-2-AM fluorescent probe tracer under a fluorescence microscope in Krebs solution containing clopiazonic acid (CPA) and nifedipin (Nif). Results: PASMCs density reached approximately to 80% in a typical valley-peak-like shape after 6 days. Cell α-smooth muscle actin (α-SMA) immunofluorescence identified that 95% of the cultured cells were PASMCs. More than 95% PASMCs responded well to calcium-potassium Krebs solution (potassium ion concentration of 60 mmol/L) and showed a rapid increase in basal [Ca(2+) ](i) after 1 minute's perfusion (Δ[Ca(2+) ](i)>50), which demonstrated that the voltage-dependent calcium channels (VDCC) of distal PASMCs were in good function; after the perfusion of calcium Krebs, calcium-free/calcium-Krebs containing CPA and Nif, distal PASMCs showed two typical peaks, indicated the full function of store-operated calcium channel (SOCC) in distal PASMCs. Conclusion: This experiment successfully established a stable and reliable mice distal PASMCs model and the study of pulmonary vascular diseases could benefit from its higher purity and better functional condition.

[The preliminary application of mNGS in the diagnosis of invasive fungal sinusitis].

Objective: By conducting a retrospective analysis of the clinical data of 14 patients diagnosed with invasive fungal rhinosinusitis (IFRS) confirmed by metagenomics next generation sequencing (mNGS) technology, we aim to explore the rapid diagnosis value of mNGS in IFRS. Methods: The clinical data of 14 IFRS patients admitted to TianJin First Central Hospital were retrospectively analyzed from February 2021 to October 2023. The study cohort comprised 8 males and 6 females, with ages ranging from 14 to 77 years. All patients were diagnosed as IFRS by performing mNGS sequencing technology of nasal sinus lesion biopsy specimens. Clinical data such as laboratory examination, imaging examination, histopathological examination results, treatment plan and prognosis were summarized and analyzed. Results: All 14 patients were diagnosed as IFRS, with mNGS detecting pathogens such as Rhizopus (7 cases), Aspergillus (5 cases), Trichoderma (1 case), and Scedosporium apiospermum (1 case). Follow-up evaluations were conducted for a period ranging from 2 months to 2 years post-treatment. At the end of follow-up, 11 out of 14 IFRS patients achieved a complete cure with no signs of recurrence, while the symptoms of the remaining 3 patients significantly improved with comprehensive treatment. Conclusion: mNGS emerges as a highly effective diagnostic tool for IFRS, providing valuable microbiological evidence for clinical diagnosis and demonstrating promising clinical utility.

Relationship of Peripheral Lymphocyte Subsets and Skeletal Muscle Mass Index in Sarcopenia: A Cross-Sectional Study.

OBJECTIVES: Lymphocytes can affect the proliferation and migration of muscle satellite cells, which may be associated with reduced muscle mass in patients with sarcopenia. The present study aimed to further enrich understandings of the changes of blood lymphocytes and explore the relationship between peripheral lymphocyte subsets and muscle mass in patients with sarcopenia. DESIGN: A cross-sectional study. SETTING: Geriatrics department of Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. METHODS: Eighty-five subjects were enrolled in this study, and were divided into two groups: the sarcopenia group (n=60) and the non-sarcopenia group (n=25). The diagnosis of sarcopenia was based on the diagnostic criteria updated by the Asian Working Group for Sarcopenia (AWGS) in 2014. Complete blood count, peripheral lymphocyte subsets, and body composition of all patients were measured. RESULTS: Skeletal muscle mass index (SMI) was negatively correlated with CD4+CD28null T lymphocytes in peripheral blood in patients with sarcopenia. CONCLUSION: The result of our study may point out the role of CD4+CD28null T lymphocytes in the pathogenesis of sarcopenia.

Protective effects of trehalose on frozen-thawed ovarian granulosa cells of cattle.

In this study, trehalose was investigated for its cryoprotective effects on ovarian granulosa cells (bGCs) of cattle. Five concentrations of trehalose at 0, 0.2, 0.4, 0.6 and 0.8 mol/L were added to the cryopreservation medium of bGCs, and the effects on the quality of frozen-thawed bGCs were assessed. The results indicate that the use of cryopreservation medium containing 0.2 and 0.4 mol/L of trehalose resulted in a greater rate of bGC viability compared to those of other groups (P<0.05). Culturing with trehalose at 0.2 and 0.4 mol/L increased 17ß- estradiol (E2)and decreased progesterone (P4)production (P < 0.05) in post-thawed bGCs. Compared with the control group, the intracellular Ca2+ concentrations of frozen-thawed bGCs were less in all treatment groups (P<0.05), and the least Ca2+ concentration was observed in the group containing 0.4 mol/L trehalose. The plasma membrane potentials of frozen-thawed bGCs were greater in the groups with 0.2 and 0.4 mol/L trehalose, and the group treated with 0.4 mol/L trehalose had the greatest membrane potential in comparison to other groups (P < 0.05). The relative abundance of the CYP19 mRNA in frozen-thawed bGCs was greater in the groups containing 0.2, 0.4 and 0.6 mol/L trehalose, and relative abundances of FSHR and BCL2 mRNA were greater in the group of bGCs treated with 0.2 mol/L trehalose (P<0.05). Trehalose treatment at 0.4, 0.6 and 0.8 mol/L had an inhibitory effect on BAX gene transcription in frozen-thawed bGCs (P<0.05). In summary, trehalose exhibited a greater cryoprotective effect on bGCs than basic cryopreservation medium.

Ultraconserved elements between the genomes of the plants Arabidopsis thaliana and rice.

Ultraconserved elements, sequences with 100% identity with no insertions or deletions between genomes, have been found in both vertebrate and invertebrate genomes; whether plant genomes contain ultraconserved elements, however, is unknown. We consequently compared the genomes of Arabidopsis thaliana and rice, which diverged about 200 million years ago, and identified 25 ultraconserved elements that are longer than 100 bp. Similar to those previously found, ultraconserved elements in plants tend to occur in clusters and locate at noncoding regions; nevertheless, they have many distinct features. For instance, the longest ultraconserved element between the 2 plant genomes is 1491 bp, much longer than the longest one (779 bp) between the human and rodent genomes. Some biological implications are discussed, but the functions of these plant ultraconserved elements and the reasons why they are practically frozen during the evolution of millions of years remain a mystery.

Fisetin Exerts Antioxidant and Neuroprotective Effects in Multiple Mutant hSOD1 Models of Amyotrophic Lateral Sclerosis by Activating ERK.

Oxidative stress exhibits a central role in the course of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease commonly found to include a copper/zinc superoxide dismutase (SOD1) gene mutation. Fisetin, a natural antioxidant, has shown benefits in varied neurodegenerative diseases. The possible effect of fisetin in ALS has not been clarified as of yet. We investigated whether fisetin affected mutant hSOD1 ALS models. Three different hSOD1-related mutant models were used: Drosophila expressing mutant hSOD1G85R, hSOD1G93A NSC34 cells, and transgenic mice. Fisetin treatment provided neuroprotection as demonstrated by an improved survival rate, attenuated motor impairment, reduced ROS damage and regulated redox homeostasis compared with those in controls. Furthermore, fisetin increased the expression of phosphorylated ERK and upregulated antioxidant factors, which were reversed by MEK/ERK inhibition. Finally, fisetin reduced the levels of both mutant and wild-type hSOD1 in vivo and in vitro, as well as the levels of detergent-insoluble hSOD1 proteins. The results indicate that fisetin protects cells from ROS damage and improves the pathological behaviors caused by oxidative stress in disease models related to SOD1 gene mutations probably by activating ERK, thereby providing a potential treatment for ALS.

Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve.

The Z curve is a three-dimensional space curve constituting the unique representation of a given DNA sequence in the sense that each can be uniquely reconstructed from the other. Based on the Z curve, a new protein coding gene-finding algorithm specific for the yeast genome at better than 95% accuracy has been proposed. Six cross-validation tests were performed to confirm the above accuracy. Using the new algorithm, the number of protein coding genes in the yeast genome is re-estimated. The estimate is based on the assumption that the unknown genes have similar statistical properties to the known genes. It is found that the number of protein coding genes in the 16 yeast chromosomes is 0.5 or YZ < 0.5, respectively. The YZ scores for all the ORFs annotated in the MIPS database have been calculated and are available on request by sending e-mail to the corresponding author.

A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences.

The occurrence frequencies of the four bases (adenine, cytosine, guanine and thymine) at each of the three codon positions for 1562 Escherichia coli protein coding sequences have been calculated. The 1562 x 4 x 3 = 18,744 data thus obtained have been analyzed by a graphic method in which the four base occurrence frequencies at each codon position for each coding sequence are represented by a point in a three-dimensional space. Thus, the 18,744 data, which would otherwise occupy several printed pages, can be intuitively displayed by a graphy. The point distribution pattern for each of the three codon positions has been analyzed. The results of our analysis indicate that the patterns for the first two codon positions reflect the origin for producing native folding structures of proteins. We thus come to the conclusion that the distribution patterns for the first two codon positions should be basically species-independent, as confirmed by studies for a number of other species. However, the distribution pattern for the third codon position is species-dependent. Based on the point distribution of the third codon position, six collective parameters have been defined to describe the overall feature of the pattern concerned. These collective parameters can be generally used to classify different species, and hence would be a useful vehicle for studies in taxonomy. In addition to E. coli, the collective parameters for a number of other species have been calculated and analyzed.

An optimization approach to predicting protein structural class from amino acid composition.

Proteins are generally classified into four structural classes: all-alpha proteins, all-beta proteins, alpha + beta proteins, and alpha/beta proteins. In this article, a protein is expressed as a vector of 20-dimensional space, in which its 20 components are defined by the composition of its 20 amino acids. Based on this, a new method, the so-called maximum component coefficient method, is proposed for predicting the structural class of a protein according to its amino acid composition. In comparison with the existing methods, the new method yields a higher general accuracy of prediction. Especially for the all-alpha proteins, the rate of correct prediction obtained by the new method is much higher than that by any of the existing methods. For instance, for the 19 all-alpha proteins investigated previously by P.Y. Chou, the rate of correct prediction by means of his method was 84.2%, but the correct rate when predicted with the new method would be 100%! Furthermore, the new method is characterized by an explicable physical picture. This is reflected by the process in which the vector representing a protein to be predicted is decomposed into four component vectors, each of which corresponds to one of the norms of the four protein structural classes.

A new quantitative criterion to distinguish between alpha/beta and alpha+beta proteins (domains).

According to the statistical analysis, it is shown that the differences of the content of alpha-helix and beta-strand between alpha/beta and alpha+beta proteins are of statistical significance. Based on the secondary structure content and the percentage of parallel or anti-parallel strands, any mixed alphabeta protein can be represented by a point in a three-dimensional prism. The distribution of the mapping points for 79 mixed alphabeta proteins (domains), of which 26 are class alpha/beta and 53 are class alpha+beta, shows that the two kinds of points are situated at distinct regions roughly. A new quantitative criterion based on the Fisher discriminant algorithm is proposed to distinguish between the alpha/beta and alpha+beta proteins (domains). Of the 79 proteins 77 are correctly classified (97.5%). As a stringent cross-validation test, the jackknife test shows that of the 79 proteins 77 are correctly classified. The jackknife test accuracy is still 97.5%. These figures indicate the self-consistence and the extrapolating effectiveness of the new quantitative criterion. Applying the new criterion to reclassify the alpha/beta and alpha+beta proteins (domains) in SCOP is also discussed. It is hoped that the new quantitative criterion will be useful for the development of protein classification databases.

Diagrammatization of codon usage in 339 human immunodeficiency virus proteins and its biological implication.

The occurrence frequencies of bases A (adenine), C (cytosine, G (guanine), and T (thymine) occurring in the 1st, 2nd, and 3rd codon positions in the codon usage table of viral genes for the 339 human immunodeficiency virus (HIV) proteins compiled recently have been calculated and diagrammatized. For comparison, the corresponding diagrammatic representations for the 2681 human proteins from the codon usage table for primate genes are also presented. The analyzed results based on these characteristic diagrams indicate that considerably similar features have been found between HIV and human proteins for the 1st and 2nd codon positions; i.e., they are all occupied predominantly by purine, especially base A. However, a significant difference in the 3rd codon position between HIV and human proteins has been observed; i.e., human proteins are of high C + G content and low A + G content in the 3rd codon position, whereas the case is just the opposite for HIV proteins. The biological implication of such a duality on the codon bias of HIV against human proteins is discussed. It is suggested that the 1st and 2nd codon positions can be termed as the structure-determining position, and the 3rd codon position termed as the species-determining position. The diagrammatic representation and analysis method described here possess a great potential for the study of molecular evolution from the viewpoint of the genetic code for which data have been accumulated rapidly and will continue to grow at a much faster pace.

Z curves, an intutive tool for visualizing and analyzing the DNA sequences.

A novel method mapping the DNA or RNA sequence into a folding curve in three dimensional space, the Z curve, has been proposed based on the symmetry of the regular tetrahedrons. There exists a unique Z curve for a given DNA sequence, on the contrary, the DNA sequence can be uniquely determined by the given Z curve. The properties of the Z curves have been studied in great details. The symmetry, the periodicity, the local motif, and the global feather of the distribution of bases of the DNA sequences are reflected by the rich folding structures of the Z curves. The Z curves may be smoothed by the B-spline functions of different orders. Therefore, the Z curves may have any resolution by choosing the suitable spline functions. The higher the order of the B-spline function chosen, the lower the resolution of the Z curve. So, the Z curves are suitable for visualizing and analyzing the DNA sequences with any length. The study of the Z curves develops further a new area to visualizing and analyzing the DNA sequences by a geometrical approach. The method of the Z curves may be strengthened by using the ripe mathematical tools of geometry on the one hand; and by using the powerful technique of the computer graphics on the other hand.

A graphic approach to evaluate algorithms of secondary structure prediction.

Algorithms of secondary structure prediction have undergone the developments of nearly 30 years. However, the problem of how to appropriately evaluate and compare algorithms has not yet completely solved. A graphic method to evaluate algorithms of secondary structure prediction has been proposed here. Traditionally, the performance of an algorithm is evaluated by a number, i.e., accuracy of various definitions. Instead of a number, we use a graph to completely evaluate an algorithm, in which the mapping points are distributed in a three-dimensional space. Each point represents the predictive result of the secondary structure of a protein. Because the distribution of mapping points in the 3D space generally contains more information than a number or a set of numbers, it is expected that algorithms may be evaluated and compared by the proposed graphic method more objectively. Based on the point distribution, six evaluation parameters are proposed, which describe the overall performance of the algorithm evaluated. Furthermore, the graphic method is simple and intuitive. As an example of application, two advanced algorithms, i.e., the PHD and NNpredict methods, are evaluated and compared. It is shown that there is still much room for further improvement for both algorithms. It is pointed out that the accuracy for predicting either the alpha-helix or beta-strand in proteins with higher alpha-helix or beta-strand content, respectively, should be greatly improved for both algorithms.

Analysis of the codon usage pattern in the Vibrio cholerae genome.

The codon usage in the Vibrio cholerae genome is analyzed in this paper. Although there are much more genes on the chromosome 1 than on chromosome 2, the codon usage patterns of genes on the two chromosomes are quite similar, indicating that the two chromosomes may have coexisted in the same cell for a very long history. Unlike the base frequency pattern observed in other genomes, the G+C content at the third codon position of the V. cholerae genome varies in a rather small interval. The most notable feature of codon usage of V. cholerae genome is that there is a fraction of genes show significant bias in base choice at the second codon position. The 2,006 known genes can be classified into two clusters according to the base frequencies at this position. The smaller cluster contains 227 genes, most of which code for proteins involved in transport and binding functions. The encoding products of these genes have significant bias in amino acids composition as compared with other genes. The codon usage patterns for the 1,836 function unknown ORFs are also analyzed, which is useful to study their functions.

A novel method to calculate the G+C content of genomic DNA sequences.

The base composition of a DNA fragment or genome is usually measured by the proportion of A+T or G+C in the sequence. The G+C content along genomic sequences is usually calculated using an overlapping or non-overlapping sliding window method. The result and accuracy of such an approach depends on the size of the window and the moving distance adopted. In this paper, a novel windowless technique to calculate the G+C content of genomic sequences is proposed. By this method, the G+C content can be calculated at different "resolution". In an extreme case, the G+C content may be computed at a specific point, rather than in a window of finite size. This is particularly useful to analyze the fine variation of base composition along genomic sequences. As the first example, the variation of G+C content along each of 16 yeast chromosomes is analyzed. The G+C-rich regions with length larger than 5 kb sequences are detected and listed in details. It is found that each chromosome consists of several G+C-rich and G+C-poor regions alternatively, i.e., a mosaic structure. Another example is to analyze the G+C content for each of the two chromosomes of the Vibrio cholerae genome. Based on the variations of the G+C content in each chromosome, it is shown that some fragments in the Vibrio cholerae genome may have been transferred from other species. Especially, the position and size of the large integron island on the smaller chromosome was precisely predicted. This method would be a useful tool for analyzing genomic sequences.

Prediction of the subcellular location of prokaryotic proteins based on the hydrophobicity index of amino acids.

An algorithm of predicting the subcellular location of prokaryotic proteins is proposed in this paper. In addition to the amino acid composition, the auto-correlation functions based on the hydrophobicity profile of amino acids along the primary sequence of the query protein have been used. Consequently, the best predictive accuracy to date has been achieved. Of the 997 prokaryotic proteins in the database used here, 688 cytoplasmic, 107 extracellular and 202 periplasmic proteins, the overall predictive accuracies are as high as 97.7 and 90.4% in the resubstitution and jackknife tests, respectively, using the hydrophilicity value of Hopp and Woods. The underlying mechanism of the improvement is also discussed. This work would be useful for a systematic analysis of the great amounts of prokaryotic genome sequences. The computer programs used in this paper are available on request via email.