A comprehensive study of the interactions in the B. subtilis degradosome with special emphasis on the role of the small proteins SR1P and SR7P.

Here, we employ coelution experiments and far-western blotting to identify stable interactions between the main components of the B. subtilis degradosome and the small proteins SR1P and SR7P. Our data indicate that B. subtilis has a degradosome comprising at least RNases Y and PnpA, enolase, phosphofructokinase, glycerol-3-phosphate dehydrogenase GapA, and helicase CshA that can be co-purified without cross-linking. All interactions were corroborated by far-western blotting with proteins purified from E. coli. Previously, we discovered that stress-induced SR7P binds enolase to enhance its interaction with and activity of enolase-bound RNase Y (RnY), while SR1P transcribed under gluconeogenic conditions interacts with GapA to stimulate its interaction with and the activity of RnjA (RnjA). We show that SR1P can directly bind RnjA, RnY, and PnpA independently of GapA, whereas SR7P only interacts with enolase. Northern blotting suggests that the degradation of individual RNAs in B. subtilis under gluconeogenic or stress conditions depends on either RnjA or RnY alone or on RnjA-SR1P, RnY-SR1P, or RnY-Eno. In vitro degradation assays with RnY or RnjA substrates corroborate the in vivo role of SR1P. Currently, it is unknown which substrate property is decisive for the utilization of one of the complexes.

Persistent sodium currents in neurons: potential mechanisms and pharmacological blockers.

Persistent sodium current (INaP) is an important activity-dependent regulator of neuronal excitability. It is involved in a variety of physiological and pathological processes, including pacemaking, prolongation of sensory potentials, neuronal injury, chronic pain and diseases such as epilepsy and amyotrophic lateral sclerosis. Despite its importance, neither the molecular basis nor the regulation of INaP are sufficiently understood. Of particular significance is a solid knowledge and widely accepted consensus about pharmacological tools for analysing the function of INaP and for developing new therapeutic strategies. However, the literature on INaP is heterogeneous, with varying definitions and methodologies used across studies. To address these issues, we provide a systematic review of the current state of knowledge on INaP, with focus on mechanisms and effects of this current in the central nervous system. We provide an overview of the specificity and efficacy of the most widely used INaP blockers: amiodarone, cannabidiol, carbamazepine, cenobamate, eslicarbazepine, ethosuximide, gabapentin, GS967, lacosamide, lamotrigine, lidocaine, NBI-921352, oxcarbazepine, phenytoine, PRAX-562, propofol, ranolazine, riluzole, rufinamide, topiramate, valproaic acid and zonisamide. We conclude that there is strong variance in the pharmacological effects of these drugs, and in the available information. At present, GS967 and riluzole can be regarded bona fide INaP blockers, while phenytoin and lacosamide are blockers that only act on the slowly inactivating component of sodium currents.

Gene-expression profiling of laser-dissected islets and studies in deficient mice reveal chemokines as differential driving force of type 1 diabetes.

Although type 1 diabetes (T1D) results from the autoimmune destruction of the insulin-producing ß-cells, its treatment is largely restricted to exogenous insulin administration. Only few therapies targeting the autoaggressive immune system have been introduced into clinical practice or are considered in clinical trials. Here, we provide a gene expression profile of the islet microenvironment obtained by laser-dissection microscopy in an inducible mouse model. Thereby, we have identified novel targets for immune intervention. Increased gene expression of most inflammatory proteins was apparent at day 10 after T1D induction and largely paralleled the observed degree of insulitis. We further focused on genes involved in leukocyte migration, including chemokines and their receptors. Besides the critical chemokine CXCL10, we found several other chemokines upregulated locally in temporary or chronic manner. Localization of the chemokine ligand/receptor pairs to the islet microenvironment has been confirmed by RNAscope. Interference with the CXCL16-CXCR6 and CX3CL1-CX3CR1 axes, but not the CCL5-CCR1/3/5 axis, resulted in reduced insulitis and lower T1D incidence. Further, we found that the receptors for the differentially expressed chemokines CXCL10, CXCL16 and CX3CL1 are distributed unevenly among islet autoantigen-specific T cells, which explains why the interference with just one chemokine axis cannot completely abrogate insulitis and T1D.

Discussion on "Bayesian meta-analysis of penetrance for cancer risk" by Thanthirige Lakshika M. Ruberu, Danielle Braun, Giovanni Parmigiani, and Swati Biswas.

Ruberu et al. (2023) introduce an elegant approach to fit a complicated meta-analysis problem with diverse reporting modalities into the framework of hierarchical Bayesian inference. We discuss issues related to some of the involved parametric model assumptions.

Fragment Orbitals Extracted from First-Principles Plane-Wave Calculations.

Decomposing extended structures into smaller, molecular, even functional groups or simple fragments has a long tradition in chemistry because it allows for understanding certain electronic peculiarities in truly chemical terms. By doing so, invaluable property information is chemically accessible, for example, needed to rationalize catalytic or magnetic or optical nature. In order to also follow that train of thought for periodic materials, we have developed a tool which in a straightforward manner derives fragment molecular orbitals from plane-wave electronic-structure data of whatever kind of solid-state material. We here report on the mathematical apparatus of the method dubbed linear combination of fragment orbitals (LCFO) used for that purpose, implemented within the LOBSTER code. The method is illustrated from various sorts of molecular entities contained in such crystalline materials, together with an assessment of both accuracy and robustness of the new tool.

Twisting DNA by salt.

The structure and properties of DNA depend on the environment, in particular the ion atmosphere. Here, we investigate how DNA twist -one of the central properties of DNA- changes with concentration and identity of the surrounding ions. To resolve how cations influence the twist, we combine single-molecule magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases monotonously with increasing concentration for all ions investigated. Second, for a given salt concentration, DNA twist strongly depends on cation identity. At 100 mM concentration, DNA twist increases as Na+ < K+ < Rb+ < Ba2+ < Li+ ≈ Cs+ < Sr2+ < Mg2+ < Ca2+. Our molecular dynamics simulations reveal that preferential binding of the cations to the DNA backbone or the nucleobases has opposing effects on DNA twist and provides the microscopic explanation of the observed ion specificity. However, the simulations also reveal shortcomings of existing force field parameters for Cs+ and Sr2+. The comprehensive view gained from our combined approach provides a foundation for understanding and predicting cation-induced structural changes both in nature and in DNA nanotechnology.

Management after acute injury of the anterior cruciate ligament (ACL). Part 3: Recommendation on surgical treatment.

PURPOSE: The aim of this consensus project was to give recommendations regarding surgical treatment of the anterior cruciate ligament (ACL) injured patient. METHODS: For this consensus process, an expert, steering and rating group was formed. In an initial online meeting, the steering group, together with the expert group, formed various key topic complexes for which multiple questions were formulated. For each key topic, a structured literature search was performed by the steering group. The results of the literature review were sent to the rating group with the option to give anonymous comments until a final consensus voting was performed. Sufficient consensus was defined as 80% agreement. RESULTS: During this consensus process, 30 topics regarding the surgical management and technique of ACL reconstruction were identified. The literature search for each key question resulted in 30 final statements. Of these 30 final statements, all achieved consensus. CONCLUSIONS: This consensus process has shown that surgical treatment of ACL injury is a complex process. Various surgical factors influence patient outcomes. The proposed treatment algorithm can be used as a decision aid for the surgeon. LEVEL OF EVIDENCE: Level V.

Extending the new era of genomic testing into pregnancy management: A proposed model for Australian prenatal services.

BACKGROUND: Trio exome sequencing can be used to investigate congenital abnormalities identified on pregnancy ultrasound, but its use in an Australian context has not been assessed. AIMS: Assess clinical outcomes and changes in management after expedited genomic testing in the prenatal period to guide the development of a model for widespread implementation. MATERIALS AND METHODS: Forty-three prospective referrals for whole exome sequencing, including 40 trios (parents and pregnancy), two singletons and one duo were assessed in a tertiary hospital setting with access to a state-wide pathology laboratory. Diagnostic yield, turn-around time (TAT), gestational age at reporting, pregnancy outcome, change in management and future pregnancy status were assessed for each family. RESULTS: A clinically significant genomic diagnosis was made in 15/43 pregnancies (35%), with an average TAT of 12 days. Gestational age at time of report ranged from 16 + 5 to 31 + 6 weeks (median 21 + 3 weeks). Molecular diagnoses included neuromuscular and skeletal disorders, RASopathies and a range of other rare Mendelian disorders. The majority of families actively used the results in pregnancy decision making as well as in management of future pregnancies. CONCLUSIONS: Rapid second trimester prenatal genomic testing can be successfully delivered to investigate structural abnormalities in pregnancy, providing crucial guidance for current and future pregnancy management. The time-sensitive nature of this testing requires close laboratory and clinical collaboration to ensure appropriate referral and result communication. We found the establishment of a prenatal coordinator role and dedicated reporting team to be important facilitators. We propose this as a model for genomic testing in other prenatal services.

Innovative trial design in precision oncology.

Genomic profiling technologies have enabled the development of targeted therapies designed to target specific biomarkers and molecular pathways involved in the pathophysiology of tumor initiation, metastasis, and drug resistance. In recent years, clinical trials with innovative design focus on the development of novel agents based on specific patient molecular alterations or other tumor characteristics and include patients with heterogenous tumor types. Precision oncology studies with innovative design associated with novel dose-finding approaches and data analysis focusing on subgroups of patients are characteristic of master protocols. Real-world data, patient-reported outcomes, and N-of-1 trials enhance the knowledge base of evidence to deliver personalized treatment to patients. Master protocols accelerate drug development by enabling simultaneous multiple sub-studies that match the patient's tumor molecular profile with experimental treatment arms. However, the increased flexibility of precision oncology trials is often associated with small subpopulations of patients, which may be underpowered to draw statistically robust conclusions. Despite their limitations, innovative clinical trials continue to rapidly translate the emerging discoveries of novel drugs into unprecedented clinical outcomes in patients with cancer and to accelerate the implementation of precision oncology.

1D Hybrid Semiconductor Silver 2,6-Difluorophenylselenolate.

Organic-inorganic hybrid materials present new opportunities for creating low-dimensional structures with unique light-matter interaction. In this work, we report a chemically robust yellow emissive one-dimensional (1D) semiconductor, silver 2,6-difluorophenylselenolate─AgSePhF2(2,6), a new member of the broader class of hybrid low-dimensional semiconductors, metal-organic chalcogenolates. While silver phenylselenolate (AgSePh) crystallizes as a two-dimensional (2D) van der Waals semiconductor, introduction of fluorine atoms at the (2,6) position of the phenyl ring induces a structural transition from 2D sheets to 1D chains. Density functional theory calculations reveal that AgSePhF2 (2,6) has strongly dispersive conduction and valence bands along the 1D crystal axis. Visible photoluminescence centered around λp ≈ 570 nm at room temperature exhibits both prompt (110 ps) and delayed (36 ns) components. The absorption spectrum exhibits excitonic resonances characteristic of low-dimensional hybrid semiconductors, with an exciton binding energy of approximately 170 meV as determined by temperature-dependent photoluminescence. The discovery of an emissive 1D silver organoselenolate highlights the structural and compositional richness of the chalcogenolate material family and provides new insights for molecular engineering of low-dimensional hybrid organic-inorganic semiconductors.

A Bayesian nonparametric approach for evaluating the causal effect of treatment in randomized trials with semi-competing risks.

We develop a Bayesian nonparametric (BNP) approach to evaluate the causal effect of treatment in a randomized trial where a nonterminal event may be censored by a terminal event, but not vice versa (i.e., semi-competing risks). Based on the idea of principal stratification, we define a novel estimand for the causal effect of treatment on the nonterminal event. We introduce identification assumptions, indexed by a sensitivity parameter, and show how to draw inference using our BNP approach. We conduct simulation studies and illustrate our methodology using data from a brain cancer trial. The R code implementing our model and algorithm is available for download at https://github.com/YanxunXu/BaySemiCompeting.

On the atomistic origin of the polymorphism and the dielectric physical properties of beryllium oxide.

Polymorphic beryllium oxide has been theoretically investigated from first principles as regards orbital occupancies, chemical bonding, polarization, as well as dielectric properties. By means of Crystal-Orbital Bond Index (COBI) analysis, the important role of the 2p orbitals on beryllium has been elucidated, in particular in terms of the correlation between polarization and beryllium-atom displacement, including the impact of the latter on the covalency of the BeO bond. In addition, several structural possibilities for a Bex Mg1-x O solid solution have been investigated for a Be content between 6% and 22%; for those, dynamically stable structures have been found, displaying large polarization values, more covalent BeO bonds, and a tendency for tetrahedral Be coordination. The dynamically unstable structures, however, resemble rock-salt BeO in their local structural properties around the Be atom. High dielectric constants and band gaps indicating insulating behavior have been found for those.

CNGPLD: case-control copy-number analysis using Gaussian process latent difference.

MOTIVATION: Cross-sectional analyses of primary cancer genomes have identified regions of recurrent somatic copy-number alteration, many of which result from positive selection during cancer formation and contain driver genes. However, no effective approach exists for identifying genomic loci under significantly different degrees of selection in cancers of different subtypes, anatomic sites or disease stages. RESULTS: CNGPLD is a new tool for performing case-control somatic copy-number analysis that facilitates the discovery of differentially amplified or deleted copy-number aberrations in a case group of cancer compared with a control group of cancer. This tool uses a Gaussian process statistical framework in order to account for the covariance structure of copy-number data along genomic coordinates and to control the false discovery rate at the region level. AVAILABILITY AND IMPLEMENTATION: CNGPLD is freely available at https://bitbucket.org/djhshih/cngpld as an R package. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quantum Chemical Similarities of Bonding in Polyiodides and Phase-Change Materials.

Covalent chemical bonding beyond the two-center two-electron (2c-2e) bond is well-known for (inter)halogenic compounds, in particular, electron-rich multicenter (or hypervalent) bonding of the three-center four-electron (3c-4e) type to explain both their structure and stability. In the present work, we examine different solid-state polyiodides by combining both local orbital wave function and projected force constant analysis in order to numerically quantify the influence of multicenter (hypervalent) bonding based on periodic density functional theory (DFT) calculations. After linking our findings to established qualitative theories on multicenter bonding, particularly, Alcock's "secondary" bonding, we relate the bonding behavior in polyiodides to industrially relevant phase-change materials of the Ge-Sb-Te class, finding further evidence for the same underlying cause as regards chemical bonding in both material classes.

Binding of Nitriles and Isonitriles to V(III) and Mo(III) Complexes: Ligand vs Metal Controlled Mechanism.

The synthesis and structures of nitrile complexes of V(N[tBu]Ar)3, 2 (Ar = 3,5-Me2C6H3), are described. Thermochemical and kinetic data for their formation were determined by variable temperature Fourier transform infrared (FTIR), calorimetry, and stopped-flow techniques. The extent of back-bonding from metal to coordinated nitrile indicates that electron donation from the metal to the nitrile plays a less prominent role for 2 than for the related complex Mo(N[tBu]Ar)3, 1. Kinetic studies reveal similar rate constants for nitrile binding to 2, but the activation parameters depend critically on the nature of R in RCN. Activation enthalpies range from 2.9 to 7.2 kcal·mol-1, and activation entropies from -9 to -28 cal·mol-1·K-1 in an opposing manner. Density functional theory (DFT) calculations provide a plausible explanation supporting the formation of a π-stacking interaction between a pendant arene of the metal anilide of 2 and the arene substituent on the incoming nitrile in favorable cases. Data for ligand binding to 1 do not exhibit this range of activation parameters and are clustered in a small area centered at ΔH‡ = 5.0 kcal·mol-1 and ΔS‡ = -26 cal·mol-1·K-1. Computational studies are in agreement with the experimental data and indicate a stronger dependence on electronic factors associated with the change in spin state upon ligand binding to 1.

A new role for SR1 from Bacillus subtilis: regulation of sporulation by inhibition of kinA translation.

SR1 is a dual-function sRNA from Bacillus subtilis. It inhibits translation initiation of ahrC mRNA encoding the transcription activator of the arginine catabolic operons. Base-pairing is promoted by the RNA chaperone CsrA, which induces a slight structural change in the ahrC mRNA to facilitate SR1 binding. Additionally, SR1 encodes the small protein SR1P that interacts with glyceraldehyde-3P dehydrogenase A to promote binding to RNase J1 and enhancing J1 activity. Here, we describe a new target of SR1, kinA mRNA encoding the major histidine kinase of the sporulation phosphorelay. SR1 and kinA mRNA share 7 complementary regions. Base-pairing between SR1 and kinA mRNA decreases kinA translation without affecting kinA mRNA stability and represses transcription of the KinA/Spo0A downstream targets spoIIE, spoIIGA and cotA. The initial interaction between SR1 and kinA mRNA occurs 10 nt downstream of the kinA start codon and is decisive for inhibition. The sr1 encoded peptide SR1P is dispensable for kinA regulation. Deletion of sr1 accelerates sporulation resulting in low quality spores with reduced stress resistance and altered coat protein composition which can be compensated by sr1 overexpression. Neither CsrA nor Hfq influence sporulation or spore properties.

Management after acute rupture of the anterior cruciate ligament (ACL). Part 1: ACL reconstruction has a protective effect on secondary meniscus and cartilage lesions.

PURPOSE: The aim of this consensus project was to validate which endogenous and exogenous factors contribute to the development of post-traumatic osteoarthritis and to what extent ACL (anterior cruciate ligament) reconstruction can prevent secondary damage to the knee joint. Based on these findings, an algorithm for the management after ACL rupture should be established. METHODS: The consensus project was initiated by the Ligament Injuries Committee of the German Knee Society (Deutsche Kniegesellschaft, DKG). A modified Delphi process was used to answer scientific questions. This process was based on key topic complexes previously formed during an initial face-to-face meeting of the steering group with the expert group. For each key topic, a comprehensive review of available literature was performed by the steering group. The results of the literature review were sent to the rating group with the option to give anonymous comments until a final consensus voting was performed. Consensus was defined a-priori as eighty percent agreement. RESULTS: Of the 17 final statements, 15 achieved consensus, and 2 have not reached consensus. Results of the consensus were summarized in an algorithm for the management after ACL rupture (infographic/Fig. 2). CONCLUSION: This consensus process has shown that the development of post-traumatic osteoarthritis is a complex multifactorial process. Exogenous (primary and secondary meniscus lesions) and endogenous factors (varus deformity) play a decisive role. Due to the complex interplay of these factors, an ACL reconstruction cannot always halt post-traumatic osteoarthritis of the knee. However, there is evidence that ACL reconstruction can prevent secondary joint damage such as meniscus lesions and that the success of meniscus repair is higher with simultaneous ACL reconstruction. Therefore, we recommend ACL reconstruction in case of a combined injury of the ACL and a meniscus lesion which is suitable for repair. LEVEL OF EVIDENCE: Level V.

Management after acute injury of the anterior cruciate ligament (ACL), part 2: management of the ACL-injured patient.

PURPOSE: The aim of this consensus project was to create a treatment algorithm for the management of the ACL-injured patient which can serve as an aid in a shared decision-making process. METHODS: For this consensus process, a steering and a rating group were formed. In an initial face-to-face meeting, the steering group, together with the expert group, formed various key topic complexes for which various questions were formulated. For each key topic, a structured literature search was performed by the steering group. The results of the literature review were sent to the rating group with the option to give anonymous comments until a final consensus voting was performed. Sufficient consensus was defined as 80% agreement. RESULTS: During this consensus process, 15 key questions were identified. The literature search for each key question resulted in 24 final statements. Of these 24 final statements, all achieved consensus. CONCLUSIONS: This consensus process has shown that ACL rupture is a complex injury, and the outcome depends to a large extent on the frequently concomitant injuries (meniscus and/or cartilage damage). These additional injuries as well as various patient-specific factors should play a role in the treatment decision. The present treatment algorithm represents a decision aid within the framework of a shared decision-making process for the ACL-injured patient. LEVEL OF EVIDENCE: Level V.

Effect of shape and size of supraspinatus tears on rotator cuff strain distribution: an in vitro study.

BACKGROUND: The impact of the size and shape of a supraspinatus tear on the strain of the intact rotator cuff and the kinematics of the shoulder is still unknown. This, however, can be relevant when deciding whether surgical reconstruction is required to prevent an increase in a tendon defect. In this study, the effect of tear width and shape on rotator cuff strain and glenohumeral kinematics was evaluated during active abduction. METHODS: Twelve fresh-frozen cadaveric shoulders with intact rotator cuffs were used in this study. We created 50% and 100% wide (full-thickness) crescent-shaped (CS) tears (n = 6) and reverse L-shaped (rLS) tears (n = 6) in the supraspinatus tendon and measured strain and kinematics during active humeral elevation until 30°. RESULTS: Both tear shapes and sizes led to an increase in internal rotation, supraspinatus loading force, and superior translation of the humerus. For the 100% wide tear size, anterior translation was observed in the CS tear group, whereas in the rLS tear group, this translation occurred mainly in the posterior direction. Strain was higher in the infraspinatus during the first 25° of abduction in comparison with the supraspinatus tendon in both tear shape groups. An analysis of the anterior and posterior tear borders showed a higher strain concentration on the same side of the tear in the CS tear group with 50% and 100% wide tears. CONCLUSIONS: The influence of different tear shapes on translation in the anterior-posterior direction was evident as both CS and rLS tears led to an oppositely directed translation of the humeral head. The strain analysis showed a stress-shielding effect of the infraspinatus at the beginning of abduction. Therefore, special attention must be paid to correctly identify the tear extension and adequately reconstruct the rotator cuff footprint. Moreover, the constant location of maximum strain in the CS tear group may lead to an earlier progression than in the rLS tear group.

Synthesis and Characterization of Iron Bispyridine Bisdicyanamide, Fe[C5H5N]2[N(CN)2]2.

Fe[C5H5N]2[N(CN)2]2 (1) was synthesized from a reaction of stoichiometric amounts of NaN(CN)2 and FeCl2·4H2O in a methanol/pyridine solution. Single-crystal and powder diffraction show that 1 crystallizes in the monoclinic space group I2/m (no. 12), different from Mn[C5H5N]2[N(CN)2]2 (P21/c, no. 14) due to tilted pyridine rings, with a = 7.453(7) Å, b = 13.167(13) Å, c = 8.522(6) Å, ß = 114.98(6)° and Z = 2. ATR-IR, AAS, and CHN measurements confirm the presence of dicyanamide and pyridine. Thermogravimetric analysis shows that π-stacking interactions of the pyridine rings play an important role in structural stabilization. Based on DFT-optimized structures, a chemical bonding analysis was performed using a local-orbital framework by projection from a plane-wave basis. The resulting bond orders and atomic charges are in good agreement with the expectations based on the structure analysis. SQUID magnetic susceptibility measurements show a high-spin state FeII compound with predominantly antiferromagnetic exchange interactions at lower temperatures.