Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins

N⁶-Methyladenosine (m⁶A) is the most abundant internal modification in RNA and is specifically recognized by YT521-B homology (YTH) domain-containing proteins. Recently we reported that YTHDC1 prefers guanosine and disfavors adenosine at the position preceding the m⁶A nucleotide in RNA and preferentially binds to the GG(m⁶A)C sequence. Now we systematically characterized the binding affinities of the YTH domains of three other human proteins and yeast YTH domain protein Pho92 and determined the crystal structures of the YTH domains of human YTHDF1 and yeast Pho92 in complex with a 5-mer m⁶A RNA, respectively. Our binding and structural data revealed that the YTH domain used a conserved aromatic cage to recognize m⁶A. Nevertheless, none of these YTH domains, except YTHDC1, display sequence selectivity at the position preceding the m⁶A modification. Structural comparison of these different YTH domains revealed that among those, only YTHDC1 harbors a distinctly selective binding pocket for the nucleotide preceding the m⁶A nucleotide.     

Activation of NF-��B Protein Prevents the Transition from Juvenile Ovary to Testis and Promotes Ovarian Development in Zebrafish

Testis differentiation in zebrafish involves juvenile ovary to testis transformation initiated by an apoptotic wave. The molecular regulation of this transformation process is not fully understood. NF-κB is activated at an early stage of development and has been shown to interact with steroidogenic factor-1 in mammals, leading to the suppression of anti-Müllerian hormone (Amh) gene expression. Because steroidogenic factor-1 and Amh are important for proper testis development, NF-κB-mediated induction of anti-apoptotic genes could, therefore, also play a role in zebrafish gonad differentiation. The aim of this study was to examine the potential role of NF-κB in zebrafish gonad differentiation. Exposure of juvenile zebrafish to heat-killed Escherichia coli activated the NF-κB pathways and resulted in an increased ratio of females from 30 to 85%. Microarray and quantitative real-time-PCR analysis of gonads showed elevated expression of NF-κB-regulated genes. To confirm the involvement of NF-κB-induced anti-apoptotic effects, zebrafish were treated with sodium deoxycholate, a known inducer of NF-κB or NF-κB activation inhibitor (NAI). Sodium deoxycholate treatment mimicked the effect of heat-killed bacteria and resulted in an increased proportion of females from 25 to 45%, whereas the inhibition of NF-κB using NAI resulted in a decrease in females from 45 to 20%. This study provides proof for an essential role of NF-κB in gonadal differentiation of zebrafish and represents an important step toward the complete understanding of the complicated process of sex differentiation in this species and possibly other cyprinid teleosts as well.     

The "beggar's" hand and the "unshakable" hand in children with total obstetric brachial plexus palsy

A total 12 consecutive children with secondary deformities following total obstetric brachial plexus palsy were included in this retrospective study. In all patients, the main complaints were two socially disabling hand postures: the "beggar's" hand and/or the "unshakable" hand. All children had a supinated forearm with no active pronation and were teased by their friends, who called them "beggars." When the impairment was severe and involved the right hand and wrist, children also complained that they were not able to shake hands. The management approach to these children was described, with the main aim of surgery being the correction of the abnormal posture. Other simultaneous tendon transfers were also performed to improve hand function if there were suitable musculotendinous units. Successful reconstruction was accomplished in all patients. Preoperatively, some children refused to go to school because of teasing, and most did not want to interact socially. After surgery, all children attended school regularly, and parents reported much better social interaction. However, the functional gain was never enough to dramatically improve the daily use of the limb. The contralateral normal limb remained the dominant one for all daily activities, including writing and eating.     

Extremely Sensitive Photonic Crystal Fiber–Based Cancer Cell Detector in the Terahertz Regime

A new photonic crystal fiber (PCF)–based, hollow-core, optical waveguide is proposed and numerically investigated to quickly identify numerous species of cancerous cells in the human body. Typical and cancerous cells have different refractive indices (RIs), and via this characteristic, the other important optical parameters are evaluated. The guiding properties of this proposed cancer cell sensor are analyzed in the COMSOL Multiphysics environment which used the finite element method as mathematical tool to solve differential equations. Furthermore, to ensure the highest simulation accuracy, extremely fine mesh elements are introduced. The simulation studies confirm that the proposed sensor, at 2.5 THz, achieves an extremely high relative sensitivity of almost 98% with negligible loss (< 0.025 dB/cm). Furthermore, a high numerical aperture (NA) and spot size, with low modal area, enhance the propagation characteristics of the sensor to a new height. The sensor’s physical structure is very simple so that it can be easily fabricated with modern fabrication technology. Thus, it seems that this sensor will open a new door in the field of detecting and diagnosing different cancer cells.

     

The Prognostic Significance of Metabolic Response Heterogeneity in Metastatic Colorectal Cancer

Background

Tumoral heterogeneity is a major determinant of resistance in solid tumors. FDG-PET/CT can identify early during chemotherapy non-responsive lesions within the whole body tumor load. This prospective multicentric proof-of-concept study explores intra-individual metabolic response (mR) heterogeneity as a treatment efficacy biomarker in chemorefractory metastatic colorectal cancer (mCRC).

Methods

Standardized FDG-PET/CT was performed at baseline and after the first cycle of combined sorafenib (600mg/day for 21 days, then 800mg/day) and capecitabine (1700 mg/m²/day administered D1-14 every 21 days). MR assessment was categorized according to the proportion of metabolically non-responding (non-mR) lesions (stable FDG uptake with SUVmax decrease <15%) among all measurable lesions.

Results

Ninety-two patients were included. The median overall survival (OS) and progression-free survival (PFS) were 8.2 months (95% CI: 6.8–10.5) and 4.2 months (95% CI: 3.4–4.8) respectively. In the 79 assessable patients, early PET-CT showed no metabolically refractory lesion in 47%, a heterogeneous mR with at least one non-mR lesion in 32%, and a consistent non-mR or early disease progression in 21%. On exploratory analysis, patients without any non-mR lesion showed a significantly longer PFS (HR 0.34; 95% CI: 0.21–0.56, P-value <0.001) and OS (HR 0.58; 95% CI: 0.36–0.92, P-value 0.02) compared to the other patients. The proportion of non-mR lesions within the tumor load did not impact PFS/OS.

Conclusion

The presence of at least one metabolically refractory lesion is associated with a poorer outcome in advanced mCRC patients treated with combined sorafenib-capecitabine. Early detection of treatment-induced mR heterogeneity may represent an important predictive efficacy biomarker in mCRC.

Trial Registration

ClinicalTrials.gov NCT01290926     

Chlorophyll fluorescence as a tool for nutrient status identification in rapeseed plants

In natural conditions, plants growth and development depends on environmental conditions, including the availability of micro- and macroelements in the soil. Nutrient status should thus be examined not by establishing the effects of single nutrient deficiencies on the physiological state of the plant but by combinations of them. Differences in the nutrient content significantly affect the photochemical process of photosynthesis therefore playing a crucial role in plants growth and development. In this work, an attempt was made to find a connection between element content in (i) different soils, (ii) plant leaves, grown on these soils and (iii) changes in selected chlorophyll a fluorescence parameters, in order to find a method for early detection of plant stress resulting from the combination of nutrient status in natural conditions. To achieve this goal, a mathematical procedure was used which combines principal component analysis (a tool for the reduction of data complexity), hierarchical k-means (a classification method) and a machine-learning method—super-organising maps. Differences in the mineral content of soil and plant leaves resulted in functional changes in the photosynthetic machinery that can be measured by chlorophyll a fluorescent signals. Five groups of patterns in the chlorophyll fluorescent parameters were established: the ‘no deficiency’, Fe-specific deficiency, slight, moderate and strong deficiency. Unfavourable development in groups with nutrient deficiency of any kind was reflected by a strong increase in F _o and ΔV/Δt ₀ and decline in φ _Po, φ _Eo δ _Ro and φ _Ro. The strong deficiency group showed the suboptimal development of the photosynthetic machinery, which affects both PSII and PSI. The nutrient-deficient groups also differed in antenna complex organisation. Thus, our work suggests that the chlorophyll fluorescent method combined with machine-learning methods can be highly informative and in some cases, it can replace much more expensive and time-consuming procedures such as chemometric analyses.     

Improving water quality in polluated drains with free water surface constructed wetlands

In Egypt, disposing of partially treated or untreated domestic and industrial wastewater into agricultural drains deteriorates their water quality. A growing interest in effective low-cost treatment of polluted water and wastewater has resulted in many studies on constructed wetlands.This study evaluates free water surface constructed wetlands (by far the largest application project is named “Lake Manzala Engineered Wetland [Egypt]”) utilized to improve the water quality in Bahr El Baqar drain, which is located at the northeastern edge of the Nile Delta. This drain discharges its water into Manzala Lake, which in turn has many fishing activities and is connected to the Mediterranean Sea. The full capacity of the constructed wetland system is 25,000 m³/day. Three various flow rate wetlands were investigated; five wetland beds of high flow rate of 0.344 m³/m²-day, five wetland beds of low flow rate of 0.048 m³/m²-day and reciprocated cells of flow of 500 m³/day.The concentrations of different contaminants along the constructed wetlands system were measured to determine the treatment efficiency. The effluent was compared with the Egyptian standards of water quality in agricultural drains (Law 48/1982). Due to the high percentage of the agricultural water drain, the concentrations of contaminants in the influent were relatively low. The percentages of removal for the different contaminants were BOD₅: 52%, COD: 50%, TSS: 87%, TDS: 32%, NH₄-N: 66%, PO₄: 52%, Fe: 51%, Cu: 36%, Zn: 47% and Pb: 52%. The natural vegetation considerably increased the value of dissolved oxygen in the treated effluent. There were little differences in the removal efficiency between the high and low flow rates beds in the system.     

Highlighting Levels of Indoxyl Sulphate among Critically Ill Patients with Acute Nephrotoxicity; Correlations Between Indoxyl Sulphate Levels and Patients’ Characteristics

Background:Many animal studies suggested that the uremic toxin indoxyl sulphate can add to renal damage following induced nephrotoxicity and this effect has not been proved in patients with such complication. Methods:This is a prospective, case-control, and an observational study conducted on 74 critically ill patients with acute nephrotoxicity. It was designed to measure serum levels of indoxyl sulphate on the day of enrollment and over the course of their illness using high performance liquid chromatography (HPLC-UV) and to test the correlation between these levels and patient’s demographics, clinical characteristics, physiological variables, and their outcomes.Results:Critically ill patients with acute nephrotoxicity had significantly higher total (tIS) and free (fIS) indoxyl sulphate than healthy controls and significantly lower than patients with end-stage renal disease (ESRD). Although, no correlation was found between tIS or fIS and mortality, among survivors, tIS, fIS, creatinine and eGFR were independently associated with no renal recovery.Conclusion:Serum indoxyl sulphate levels were elevated in critically ill patients with acute nephrotoxicity. There is an association between high levels of indoxyl sulphate and no renal-recovery outcome among survivors of acute nephrotoxicity. Early removal of indoxyl sulphate from patients’ blood may improve their outcomes.Key Words: HPLC, Indoxyl sulphate, Mortality, Prognosis, Toxic acute kidney injury