Host-modifying drugs against COVID-19: some successes,but not yet the breakthrough

After reviewing antiviral drugs (Brüssow Environmental Microbiology 2021) the present review summarizes the results of clinical trials with host-modifying drugs in COVID-19 patients. Clinical benefits were observed with different immunomodulators. The variable outcomes of trials with the interleukin 6 receptor inhibitor tocilizumab demonstrated that treatment benefits might only be present in specific subgroups of patients or in specific infection stages. A meta-analysis of trials with the interleukin 1 receptor antagonist anakinra showed a survival benefit only in patients with hyperinflammation. The Janus kinase inhibitor baricitinib is an anti-inflammatory treatment that showed a clinical benefit in hospitalized patients who do not yet need supplementary oxygen. In contrast, the corticosteroid dexamethasone showed mortality reducing effects that were limited to patients on ventilation or in need of supplementary oxygen. Therapeutic dose of anticoagulation met the criteria for inferiority in severe cases, but showed a small survival benefit in non-severe COVID-19 patients. Large trials with colchicine showed a small or no survival benefit. Azithromycin, an antibiotic with immunomodulatory activity, showed no effects in numerous clinical trials. The trials showed a clear need for new drugs instead of repurposed drugs and drugs that specifically target the SARS-CoV-2 virus or the pathology developing in COVID-19 patients.     

Droplet centrifugation,droplet DNA extraction,and rapid droplet thermocycling for simpler and faster PCR assay using wire-guided manipulations

ABSTRACT: A computer numerical control (CNC) apparatus was used to perform droplet centrifugation, droplet DNA extraction, and rapid droplet thermocycling on a single superhydrophobic surface and a multi-chambered PCB heater. Droplets were manipulated using "wire-guided" method (a pipette tip was used in this study). This methodology can be easily adapted to existing commercial robotic pipetting system, while demonstrated added capabilities such as vibrational mixing, high-speed centrifuging of droplets, simple DNA extraction utilizing the hydrophobicity difference between the tip and the superhydrophobic surface, and rapid thermocycling with a moving droplet, all with wire-guided droplet manipulations on a superhydrophobic surface and a multi-chambered PCB heater (i.e., not on a 96-well plate). Serial dilutions were demonstrated for diluting sample matrix. Centrifuging was demonstrated by rotating a 10 muL droplet at 2300 round per minute, concentrating E. coli by more than 3-fold within 3 min. DNA extraction was demonstrated from E. coli sample utilizing the disposable pipette tip to cleverly attract the extracted DNA from the droplet residing on a superhydrophobic surface, which took less than 10 min. Following extraction, the 1500 bp sequence of Peptidase D from E. coli was amplified using rapid droplet thermocycling, which took 10 min for 30 cycles. The total assay time was 23 min, including droplet centrifugation, droplet DNA extraction and rapid droplet thermocycling. Evaporation from of 10 muL droplets was not significant during these procedures, since the longest time exposure to air and the vibrations was less than 5 min (during DNA extraction). The results of these sequentially executed processes were analyzed using gel electrophoresis. Thus, this work demonstrates the adaptability of the system to replace many common laboratory tasks on a single platform (through re-programmability), in rapid succession (using droplets), and with a high level of accuracy and automation.     

How to climb a tree: lizards accelerate faster,but pause more,when escaping on vertical surfaces

Many species of lizards effectively traverse both two and three‐dimensional habitats. However, few studies have examined maximum locomotor performance on different inclines. Do maximum acceleration and velocity differ on a level and inclined surface? Do lizards pause more on an inclined surface? To address these questions, Sceloporus woodi lizards (N = 12) were run in the laboratory on a level trackway and a vertical tree trunk. This species is known to frequently utilize both vertical and horizontal aspects of its habitat. Average maximum acceleration on the vertical surface exceeded that on the level surface, although average maximum velocity exhibited the opposite pattern. The average number of pauses during level locomotion was lower compared to vertical locomotion. In addition, the average location of the first pause on the level surface was 0.51 m, which is farther than the average for vertical locomotion where the first pause was at 0.35 m. The combination of performance and pause data suggests that the relative lack of pausing during level locomotion allows individuals to reach higher maximum velocities on level surfaces because they accelerate over greater distances. The increased pausing when moving vertically could be a result of high energetic demands of vertical locomotion, or greater microhabitat complexity as a result of branching and/or refuges. The faster acceleration exhibited during vertical locomotion by S. woodi likely offsets the frequent pauses. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 83–90.     

Neural induction: old problem, new findings, yet more questions

During neural induction, the embryonic neural plate is specified and set aside from other parts of the ectoderm. A popular molecular explanation is the 'default model' of neural induction, which proposes that ectodermal cells give rise to neural plate if they receive no signals at all, while BMP activity directs them to become epidermis. However, neural induction now appears to be more complex than once thought, and can no longer be fully explained by the default model alone. This review summarizes neural induction events in different species and highlights some unanswered questions about this important developmental process.     

A new simpler photoaffinity analogue of peptidyl tRNA

The synthesis of the n-hydroxysuccinimide ester of N-(2-nitro-4-azidophenyl)glycine (NAG) is described. This reacts with E. coli phe-tRNA(Phe) to yield the photoaffinity label NAG-Phe-tRNA(Phe). This peptidyl tRNA analogue binds correctly to the peptidyl site of the E. coli ribosome. The only significant covalent products found after irradiation of a peptidyl site bound NAG-Phe-tRNA(Phe)-70S-poly(U) complex are 50S proteins L11 and L18. After irradiation the complex can still bind [(3)H]Phe-tRNA to the amino acyl site and participate in peptide bond formation with the covalently attached NAG-Phe moiety. Alternatively, one can allow peptide bond formation to occur first, prior to photolysis. The reaction products are still L11 and L18. Hence, both of these two proteins appear to be centrally located at the peptidyl transferase center.     

Ontogeny of sexual size dimorphism in monitor lizards: males grow for a longer period, but not at a faster rate

Monitor lizards belong to the largest and the most sexually dimorphic lizards in terms of size, making this group an ideal model for studies analyzing ontogenetic causes of sexual dimorphism. Understanding of these ontogenetic factors is essential to the current discussion concerning patterns of sexual dimorphism in animals. We examined the ontogenetic trajectories of body weight and snout-vent length to analyze the emergence of sexual size dimorphism. Experimental animals were 22 males and 13 females of mangrove-dwelling monitors (Varanus indicus) hatched at the Prague Zoo. They were regularly weighed and measured up to the age of 33-40 months, and subsequently sexed by ultrasonographic imaging. The logistic growth equation was used to describe and analyze the observed growth patterns. Our results confirm considerable sexual size dimorphism in the mangrove monitor. The mean asymptotic body weight of males was nearly three times higher than that of females. As the body size of male and female hatchlings is almost equal, and the growth rate parameter (K) of the logistic growth equation as well as the absolute growth rate up to the age of 12 months do not differ between the sexes, size differences between fully grown males and females should be attributed to timing of the postnatal growth. Males continue to grow several months after they reach the age when the growth of females is already reduced. Therefore, the sexual size dimorphism emerges and sharply increases at this period.     

HIV vaccine: it may take two to tango, but no party time yet

In a recent summary of integrase sequences, primary integrase inhibitor mutations were rare. In a review of integrase inhibitor-naïve Australian HIV-1 sequences, primary mutations were not identified, although the accessory mutation G140S was detected. A link with previous antiretroviral therapy, intra-subtype B divergence across the integrase gene and transmission of integrase polymorphisms were also noted. Based on these findings, we would recommend ongoing surveillance of integrase mutations, and integrase region sequencing for patients prior to commencement of integrase inhibitors.     

Identifying gastropod spawn from DNA barcodes: possible but not yet practicable

Identifying life stages of species with complex life histories is problematic as species are often only known and/or described from a single stage. DNA barcoding has been touted as an important tool for linking life-history stages of the same species. To test the current efficacy of DNA barcodes for identifying unknown mollusk life stages, 24 marine gastropod egg capsules were collected off the Philippines in deep water and sequenced for partial fragments of the COI, 16S and 12S mitochondrial genes. Two egg capsules of known shallow-water Mediterranean species were used to calibrate the method. These sequences were compared to those available in GenBank and the Barcode of Life Database (BOLD). Using COI sequences alone, only a single Mediterranean egg capsule was identified to species, and a single Philippine egg capsule was identified tentatively to genus; all other COI sequences recovered matches between 76% and 90% with sequences from BOLD and GenBank. Similarity-based identification using all three markers confirmed the Mediterranean specimens' identifications. A phylogenetic approach was also implemented to confirm similarity-based identifications and provide a higher-taxonomic identification when species-level identifications were not possible. Comparison of available GenBank sequences to the diversity curve of a well-sampled coral reef habitat in New Caledonia highlights the poor taxonomic coverage achieved at present in existing genetic databases, emphasizing the need to develop DNA barcoding projects for megadiverse and often taxonomically challenging groups such as mollusks, to fully realize its potential as an identification and discovery tool.     

Genetic similarity of polyploids: a new version of the computer program POPDIST (version 1.2.0) considers intraspecific genetic differentiation

For evolutionary studies of polyploid species estimates of the genetic identity between species with different degrees of ploidy are particularly required because gene counting in samples of polyploid individuals often cannot be done, e.g., in triploids the phenotype AB can be genotypically either ABB or AAB. We recently suggested a genetic distance measure that is based on phenotype counting and made available the computer program POPDIST. The program provides maximum-likelihood estimates of the genetic identities and distances between polyploid populations, but this approach is not informative for populations within species that only differ in their allele frequencies. We now close this gap by applying the frequencies of shared 'bands' in both populations to Nei's identity measure. Our simulation study demonstrates the close correlation between the band-sharing identity and the genetic identity calculated on the basis of gene frequencies for any degree of ploidy. The new extended version of POPDIST (version 1.2.0) provides the option of choosing either the maximum-likelihood estimator or the band-sharing measure.