Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group

The Bacillus cereus group comprises the four valid species Bacillus cereus, Bacillus mycoides, Bacillus thuringiensis and bacillus anthracis. Some isolates of B. cereus are known to be psychrotolerant (growth at 7 degrees C or below). Here, specific sequence differences are described between the 16S rDNA, the 23S rDNA, the 16S-23S rDNA spacer region and the genes of the major cold-shock protein homologue cspA in a variety of psychrotolerant and mesophilic B. cereus and B. mycoides strains. Randomly amplified polymorphic DNA analysis using three different primers clearly separated psychrotolerant strains of both species from the rest of the B. cereus group, as did inverse PCR patterns of the rDNA operons. These data strongly support a hitherto unrecognized fifth sub-group within the B. cereus species group comprising psychrotolerant, but not mesophilic, B. cereus strains. Despite the latter finding, the DNA sequences investigated exhibited a high degree of sequence similarity indicating a close relationship between the species of the B. cereus group. Considering the unusual importance of B. cereus in both food poisoning and food spoilage and to avoid merging all species of the group, a new species, Bacillus weihenstephanensis sp. nov., comprising psychrotolerant 'cereus' strains, is proposed. Isolates of the new species grow at 4-7 degrees C but not at 43 degrees C and can be identified rapidly using rDNA or cspA targeted PCR. The type strain is B. weihenstephanensis WSBC 10204T (= DSM 11821T).

A controlled family history study of prepubertal major depressive disorder

First-degree (N = 195) and second-degree (N = 785) adult relatives of prepubertal children with major depression (N = 48), children with nonaffective psychiatric disorders (N = 20), and normal children (N = 27) were assessed by the Family History-Research Diagnostic Criteria method (FH-RDC), except for the adult informant (usually the mother), who was directly interviewed. Compared with normal controls, prepubertal children with major depressive disorder (MDD) had significantly higher familial rates of psychiatric disorders in both first- and second-degree relatives, especially MDD, alcoholism, and "other" (mostly anxiety) diagnoses. Relatives of children in the nonaffective psychiatric control (PC) group had low rates of alcoholism, high rates of other (anxiety) disorder diagnoses, and intermediate rates of MDD (accounted for by those children with separation anxiety). This suggests that prepubertal onset of major depression may be especially likely in families with a high aggregation of affective disorders when these families also have a high prevalence of alcoholism, and that a proportion of children without affective disorder but with separation anxiety disorder in this study were at high risk for the development of affective illness later in life. These results support the validity of prepubertal-onset depressive illness as a diagnostic category, and are consistent with high familial rates of MDD and other psychiatric disorders found in family studies of adolescent and early-onset adult probands with major affective disorders, and with studies of the offspring of parents with major affective disorders. Within the child MDD group substantial heterogeneity was found. Low familial rates of MDD were associated with suicidality and comorbid conduct disorder in the child probands. The highest familial rates of MDD, approximately threefold those in the normal controls, and all the bipolar relatives, were found in the families of prepubertal probands with MDD who never had a concrete suicidal plan or act and who were without comorbid conduct disorder. A useful nosological continuum in which to classify prepubertal MDD may be to place at one end those patients with comorbid conduct disorder and at the other end those patients with manifestations related to bipolarity, including hypomania, mania, and psychotic subtype.

Identification and purification of a family of dimeric major cold shock protein homologs from the psychrotrophic Bacillus cereus WSBC 10201

Whole-cell protein patterns of a psychrotrophic Bacillus cereus strain from cultures grown at 7 and 30 degrees C were compared. This analysis revealed that at least three major proteins are expressed at a significantly higher rate at 7 degrees C than at 30 degrees C. The most abundant of these cold-induced proteins was a small polypeptide of 7.5 kDa, designated CspA, of B. cereus. In addition, four small proteins very similar in size to CspA were seen on both 7 degrees C and 30 degrees C two-dimensional protein gels. Immunoblot analysis using B. cereus anti-CspA antibodies indicated that the five proteins described above plus an additional sixth protein not visible on silver-stained two-dimensional gels are members of a B. cereus cold shock protein family. This hypothesis was corroborated by cloning and sequencing of the genes encoding five proteins of this family. The protein sequences deduced are highly similar and show homology to small procaryotic cold shock proteins and to the cold shock domain of eucaryotic Y-box proteins. Besides CspA, only one of the additional five CspA homologs was slightly cold inducible. In the presence of 100 mM NaCl, the two purified members of the protein family (CspA and CspE) elute as dimers at an apparent molecular mass of 15 kDa from a gel filtration column. At higher salt concentrations, they dissociate into their monomers. Their ability to bind to the ATTGG motif of single-stranded oligonucleotides was demonstrated by band shift analysis.

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments

The PSI-BLAST algorithm has been acknowledged as one of the most powerful tools for detecting remote evolutionary relationships by sequence considerations only. This has been demonstrated by its ability to recognize remote structural homologues and by the greatest coverage it enables in annotation of a complete genome. Although recognizing the correct fold of a sequence is of major importance, the accuracy of the alignment is crucial for the success of modeling one sequence by the structure of its remote homologue. Here we assess the accuracy of PSI-BLAST alignments on a stringent database of 123 structurally similar, sequence-dissimilar pairs of proteins, by comparing them to the alignments defined on a structural basis. Each protein sequence is compared to a nonredundant database of the protein sequences by PSI-BLAST. Whenever a pair member detects its pair-mate, the positions that are aligned both in the sequential and structural alignments are determined, and the alignment sensitivity is expressed as the percentage of these positions out of the structural alignment. Fifty-two sequences detected their pair-mates (for 16 pairs the success was bi-directional when either pair member was used as a query). The average percentage of correctly aligned residues per structural alignment was 43.5+/-2.2%. Other properties of the alignments were also examined, such as the sensitivity vs. specificity and the change in these parameters over consecutive iterations. Notably, there is an improvement in alignment sensitivity over consecutive iterations, reaching an average of 50.9+/-2.5% within the five iterations tested in the current study.

Lesions of excitatory pathways reduce hippocampal cell death after transient forebrain ischemia in the gerbil

Transient forebrain ischemia produces a spatially and temporally selective pattern of neuronal degeneration in the hippocampal formation of the Mongolian gerbil. Ischemic neuronal death has been suggested to depend on the activation of excitatory hippocampal pathways that project to the vulnerable neurons. This idea was tested by examining the effect of a unilateral entorhinal cortical lesion or a unilateral knife cut lesion of intrahippocampal pathways on the neuropathology produced by 5 min of complete forebrain ischemia. A prior lesion of either the ipsilateral entorhinal cortex or the mossy fiber and Schaffer collateral-commissural pathways partially prevented the destruction of CA1b pyramidal cells in most animals. It did not, however, reduce the extent of ischemic neuronal death in any other hippocampal subfield. Within area CA1b, an entorhinal lesion protected an average of 23% of the pyramidal cells and a transection of both mossy and Schaffer collateral-commissural fibers protected an average of 36.5%. CA1b pyramidal cells saved from ischemia-induced degeneration appeared clearly abnormal when stained with cresyl violet or by silver impregnation. It is suggested that lesions of excitatory pathways attenuate ischemic damage to area CA1b by directly or indirectly reducing the level of synaptic excitation onto the vulnerable neurons. However, only a relatively small percentage of hippocampal neurons can be protected by these lesions in the gerbil ischemia model and there is reason to believe that the neurons protected in this manner may not be electrophysiologically competent. Synaptic excitation therefore appears to play an important, but not an essential, role in this model of ischemic brain damage.

Father kills mother. Issues and problems encountered by a child psychiatric team

The child whose mother is killed by his or her father has to cope with the trauma of violence, the grief associated with the loss of both parents simultaneously, dislocation and insecurity regarding where and with whom they will live, stigma, secrecy, and often massive conflicts of loyalty. These issues and how they affected the 28 children of 14 families in which the father had killed the mother are examined. Recommendations for practice based on this clinical experience are proposed.

CIS: compound importance sampling method for protein-DNA binding site p-value estimation

MOTIVATION

A key aspect of transcriptional regulation is the binding of transcription factors to sequence-specific binding sites that allow them to modulate the expression of nearby genes. Given models of such binding sites, one can scan regulatory regions for putative binding sites and construct a genome-wide regulatory network. In such genome-wide scans, it is crucial to control the amount of false positive predictions. Recently, several works demonstrated the benefits of modeling dependencies between positions within the binding site. Yet, computing the statistical significance of putative binding sites in this scenario remains a challenge.

RESULTS

We present a general, accurate and efficient method for computing p-values of putative binding sites that is applicable to a large class of probabilistic binding site and background models. We demonstrate the accuracy of the method on synthetic and real-life data.

AVAILABILITY

The procedure for scanning DNA sequences and computing the statistical significance of putative binding site scores is available upon request at http://compbio.cs.huji.ac.il/CIS/ CONTACT: nir@cs.huji.ac.il.

Father kills mother: post-traumatic stress disorder in the children

Results of a study of over 100 children whose father killed their mother have been summarized and principles for practice have been formulated. All children orphaned by the death of one parent at the other's hands should be seen as soon as possible in a child psychiatry department and assessed. An immediate crisis intervention will probably be needed if they witnessed the killing to prevent PTSD. Bereavement counselling will be helpful in most cases. The caretakers will need support and help with their own mourning. Placement, access and custody, compensation, seeing the body, attending the funeral and dealing with family conflict will all need consideration. Long-term follow-up and further research are recommended.

Comparison of results after surgical repair of acute and chronic ulnar collateral ligament injury of the thumb

This study sought to demonstrate that successful outcomes can be achieved with the new technique presented here for chronic ulnar collateral ligament (UCL) injury of the thumb metacarpophalangeal (MCP) joint, as well as with K-wire pinning for acute UCL injury. We followed 19 patients who suffered an UCL rupture (mean follow-up: 14.26±4.65 months) and 32 patients who presented with UCL avulsion fracture (mean follow-up: 16.81±7.54 months). We used a free tendon graft for UCL reconstruction in the UCL rupture group. Both ends of the graft were stabilized with bioabsorbable suture anchors, which were used as biotenodesis interference screws. Closed reduction and K-wire fixation was used in UCL avulsion fracture group. There were no statistically significant differences between operated and contralateral healthy thumb MCP joint in both groups in the grip strength, tip pinch strength, flexion, extension, ulnar deviation, and radial deviation movements at final follow-up. Grip strength, tip pinch strength, ulnar deviation and radial deviation were significantly better in the avulsion group than the rupture group. All patients regained full stability at the MCP joint in avulsion group; 16 patients regained full stability and 3 patients presented with mild laxity (less than 10° laxity) in rupture group. Glickel grading scale used as a functional score was excellent for 30 patients and good for 2 patients in avulsion group; it was excellent for 17 patients and good for 2 patients in rupture group. Our study shows that closed reduction and percutaneous K-wire fixation of acute displaced large UCL avulsion fracture is a simple technique and achieves adequate stability of UCL. For UCL rupture, free tendon reconstruction with bioabsorbable suture anchors provides adequate stability and stable fixation within the tunnels.

Plasma lipid levels in active and sedentary premenopausal females

Cross-sectional data on 19 long-distance runners (LD), 17 aerobic dancers (AD), 19 recreational joggers (RJ), and 15 inactive controls (IC) were examined for cardiovascular endurance and determination of plasma lipoproteins. Subjects included premenopausal eumenorrheic females who were non-smokers and presently not using oral contraceptives. Results indicated that all groups were similar in age, height and weight. Only the AD group had a significantly lower percent body fat (p less than .001) than the other groups. The LD, AD and RJ groups had a significantly higher VO2max than the IC group (p less than .05), and the LD and AD groups had a significantly higher VO2max than the RJ group (p less than .05). Analysis of a one-day food log indicated that the only difference in diet among the groups was a significantly lower intake of total and monounsaturated fat in the AD group (p less than .05) and a significantly lower intake of carbohydrates in the IC group than the AD group (p less than .05). Analysis of plasma lipids revealed no significant differences in any lipid variables among the groups. These findings indicate that healthy premenopausal eumenorrheic females with similar physical characteristics also have similar plasma lipid profiles regardless of their physical activity level.

Marital conflict by proxy after father kills mother: the family therapist as an expert witness in court

The father killing the mother leaves the children effectively without parents. The extended family from both sides will often intervene to offer a home for the children, or at least to have a say in what arrangements are made for the children and how they are to be brought up. Intensely competitive and hostile feelings between the opposing sets of relatives are commonly aroused, and the children may be caught up in a battle reminiscent of the conflict between their parents, which culminated in the death of their mother. I and my colleagues have, as a team, seen more than 300 children who have lost one parent at the hands of the other, and we have been involved in subsequent custody battles as expert witnesses. Based on this experience and using this context as an example, the issues for the family therapist as expert witness in adversarial Court proceedings are presented. A case is described that illustrates the theoretical exposition--including the effectiveness of family therapy from the witness box.