Hydrophobic core formation in protein complex of cathepsin

The “fuzzy oil drop” model assumes that the idealized hydrophobic core in a protein body can be described by a 3D Gauss function. The structure of the 1ICF protein (cathepsin), which participates in the proteolysis process and has cysteine-type peptidase activity, has been analyzed on the basis of the “fuzzy oil drop” model. The authors have determined the contribution of individual exon fragments to the creation of a common hydrophobic core and assessed the involvement of each chain in this process, depending on the number of complexed chains. Quantitative assessment of exons, chains, dimers, and the whole complex suggest that each of these units plays a different role in shaping the protein’s hydrophobic core.     

Why is sex so rare in Lecane inermis (Rotifera: Monogononta) in wastewater treatment plants?

The monogonont rotifer Lecane inermis is commonly known as a facultative parthenogen. Unexpectedly, among numerous lineages we isolated from wastewater treatment plants (WWTP), only one was capable of sexual reproduction. We investigated why sex was so rare among L. inermis in WWTP. The reproductive modes of lineages derived from the sexual lineage were examined. Among all lineages, the fraction of those reproducing only asexually for 14 d was 0.39. In the subsequent round, the fraction of asexual lineages reached 0.61. The population growth rate of the parthenogenetic lineages was significantly higher than that of the sexual lineages. We simulated the fate of rotifer populations in WWTP by removing 10% of the experimental cultures each day. After 10 d of these conditions, the mean number of females was greater in parthenogenetic than in sexual lineages. After 20 d, only solitary dormant eggs remained in the sexual lineages. It therefore appears that the loss of sex may be attributed to the specific conditions of the WWTP. When there is no risk of desiccation and no need for dormancy, the fast‐growing parthenogens outcompete lineages investing in costly sex. Furthermore, even if some resting eggs were deposited, they would be washed out from the system with the excess sludge.     

Systemic changes in photosynthesis and reactive oxygen species homeostasis in shoots of Arabidopsis thaliana infected with the beet cyst nematode Heterodera schachtii

Photosynthetic efficiency and redox homeostasis are important for plant physiological processes during regular development as well as defence responses. The second‐stage juveniles of Heterodera schachtii induce syncytial feeding sites in host roots. To ascertain whether the development of syncytia alters photosynthesis and the metabolism of reactive oxygen species (ROS), chlorophyll a fluorescence measurements and antioxidant responses were studied in Arabidopsis thaliana shoots on the day of inoculation and at 3, 7 and 15 days post‐inoculation (dpi). Nematode parasitism caused an accumulation of superoxide and hydrogen peroxide molecules in the shoots of infected plants at 3 dpi, probably as a result of the observed down‐regulation of antioxidant enzymes. These changes were accompanied by an increase in RNA and lipid oxidation markers. The activities of antioxidant enzymes were found to be enhanced on infection at 7 and 15 dpi, and the content of anthocyanins was elevated from 3 dpi. The fluorescence parameter R_fd, defining plant vitality and the photosynthetic capacity of leaves, decreased by 11% only at 7 dpi, and non‐photochemical quenching (NPQ), indicating the effectiveness of photoprotection mechanisms, was about 16% lower at 3 and 7 dpi. As a result of infection, the ultrastructure of chloroplasts was changed (large starch grains and plastoglobules), and more numerous and larger peroxisomes were observed in the mesophyll cells of leaves. We postulate that the joint action of antioxidant enzymes/molecules and photochemical mechanisms leading to the maintenance of photosynthetic efficiency promotes the fine‐tuning of the infected plants to oxidative stress induced by parasitic cyst nematodes.     

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination

Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the “elbow” regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab–antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones.     

Difficulties in identifying the bacterial species from the genus <Emphasis Type="Italic">Clostridium</Emphasis> in a case of injury-related osteitis

Most Clostridium species are part of saprophytic microflora in humans and animals; however, some are well-known human pathogens. We presented the challenges in identifying the Clostridium species isolated from a patient with an infected open dislocation of the proximal interphalangeal joint of the fourth digit of the right hand. The clinical materials were intraoperative samples collected from a patient diagnosed with an injury-related infection, with soft tissue loss and tendon sheath involvement. The available biochemical, molecular, and genetic techniques were used in identifying the isolated bacteria. The isolated bacterium was shown to have low biochemical activity; hence, it was not definitively identified via biochemical tests Api 20A or Rapid 32A. Vitek 2 and mass spectrometry methods were equally inconclusive. Clostridium tetani infection was strongly suspected based on the bacterium’s morphology and the appearance of its colonies on solid media. It was only via the 16S rRNA sequencing method, which is non-routine and unavailable in most clinical laboratories, that this pathogen was excluded. Despite appropriate pre-laboratory procedures, which are critical for obtaining reliable test results, the routine methods of anaerobic bacterium identification are not always useful in diagnostics. Diagnostic difficulties occur in the case of environment-derived bacteria of low or not fully understood biological activity, which are absent from databases of automatic bacterial identification systems.     

Novel (S)-1,3,4,12a-tetrahydropyrazino[2,1-c][1,4]benzodiazepine-6,12(2H,11H)-dione derivatives: Selective inhibition of MV-4-11 biphenotypic B myelomonocytic leukemia cells’ growth is accompanied by reactive oxygen species overproduction and apoptosis

A series of optically pure (R)- and (S)-1,3,4,12a-tetrahydropyrazino[2,1-c][1,4]benzodiazepine-6,12(2H,11H)-dione derivatives was designed and synthesized as novel anthramycin analogues in a three-step, one-pot procedure, and tested for their antiproliferative activity on nine following cell lines: MV-4-11, UMUC-3, MDA-MB-231, MCF7, LoVo, HT-29, A-549, A2780 and BALB/3T3. The key structural features responsible for exhibition of cytotoxic effect were determined: the (S)-configuration of chiral center and the presence of hydrophobic 4-biphenyl substituent in the side chain. Introduction of bromine atom into the 8 position (8g) or substitution of dilactam ring with benzyl group (8m) further improved the activity and selectivity of investigated compounds. Among others, compound 8g exhibited selective cytotoxic effect against MV-4-11 (IC₅₀?=?8.7?μM) and HT-29 (IC₅₀?=?17.8?μM) cell lines, while 8m showed noticeable anticancer activity against MV-4-11 (IC₅₀?=?10.8?μM) and LoVo (IC₅₀?=?11.0?μM) cell lines. The cell cycle arrest in G₁/S checkpoint and apoptosis associated with overproduction of reactive oxygen species was also observed for 8e and 8m.     

Solid-stemmed spring wheat cultivars give better androgenic response than hollow-stemmed cultivars in anther culture

Solid-stemmed spring wheat cultivars (Triticum aestivum L.) are resistant to the stem sawfly (Cephus cinctus Nort.) and lodging. Anthers of 24 spring wheat cultivars with varying content of pith in the stem were used in the experiment. All were classified into three groups: solid, medium–solid and hollow stems. There was considerable influence of the cultivar on callus formation and green plant regeneration. The highest efficiency of green plant regeneration (24%) was observed for the solid-stemmed AC Abbey cultivar. There was no regeneration from the explants of four cultivars: CLTR 7027, Alentejano, Marquis and Bombona. Principal component analysis showed no differences between the cases under observation (callus induction and green plant regeneration) in their response to pre-treatment temperatures (4 and 8°C). The examination of the effects of various auxin types in the induction medium on callus formation and green plant regeneration revealed that the strongest stimulation of these processes was observed in the C17 medium with 2,4-D and dicamba. The efficiency of callus formation and green plant regeneration was greater in solid-stemmed cultivars than in hollow-stemmed cultivars.     

Fine-Needle Aspiration Biopsy as a Preoperative Procedure in Patients with Malignancy in Solitary and Multiple Thyroid Nodules

Background

Fine-needle aspiration biopsy (FNAB) is a recognized technique for the basic, preoperative cytological diagnosis of thyroid nodules.

Aim of the Study

To analyze the accuracy of FNAB in the diagnosis of thyroid cancer in patients with solitary and multiple thyroid nodules and to compare the demographic, clinical and pathological characteristics of patients with thyroid carcinoma in solitary and multiple tumors.

Materials and Methods

The case records of 2,403 patients with solitary and multiple thyroid tumors treated consecutively between 2008 and 2013 were analyzed retrospectively. We selected 1,645 for further analysis. A solitary thyroid nodule was observed in 493 patients, and multiple nodules were detected in 1,152 patients. Further classification of the patients in these two groups was performed on the basis of the FNAB results, type of surgery performed and histopathology. TC was histopathologically confirmed in 166 patients, and benign disease was found in 1,479. The TC patients were assigned to the study group, and those with benign thyroid disease were placed into the control group. The study group was divided into two subgroups according to the presence of cancer in a single thyroid nodule or in multiple nodules. Malignancy in a solitary thyroid nodule was diagnosed in 98 (59.0%) patients, and cancer in multiple nodules was diagnosed in 68 (41.0%). Comparative analyses of the demographic, clinical and histopathological characteristics were performed for both subgroups. The following statistical analyses were performed: comparative characteristic of subgroups, ROC analysis for study group and subgroup of patients, and multivariable logistic regression analysis for study group.

Results

The rate of prediction of TC by FNAB was three times higher in the patients with a solitary thyroid nodule compared with those with multiple thyroid nodules and it was statistically significant (p<0.001). The rate of total thyroid resection and lack of necessity for reoperation were also significantly higher in the TC patients with a solitary nodule. The histopathological results showed that significantly more patients with a solitary nodule had advanced-stage TC (stage III or IV) and tumor progression (pT3 or pT4) (p = 0.002 for both). ROC analysis demonstrated that the overall accuracy of FNAB as a predictor of thyroid cancer presence was high, especially for the subgroup of patients with a solitary thyroid nodule (AUC = 0.958, p<0.0001). Multivariable logistic regression analysis confirmed that a positive FNAB result was the sole predictor of the performance of total resection in the TC study group (p<0.0001), while a negative FNAB result and the presence of a papillary cancer type were independent predictors of the risk of reoperation (p<0.0001 and p = 0.002, respectively).

Conclusions

FNAB often produces false-negative results in patients with multiple malignant thyroid tumors, which results in reoperation in many cases. False-negative FNAB results are rare in patients with a solitary tumor. Because of the low predictive capacity of FNAB for thyroid cancer in patients with multiple thyroid tumors, total thyroid excision should be considered in most cases despite a "negative" (no malignant) FNAB result.