Balanced assessment of growth disorders using clinical, endocrinological, and genetic approaches

Determining the pathogenesis of pediatric growth disorders is often challenging. In many cases, no pathogenesis is identified, and a designation of idiopathic short stature is used. The investigation of short stature requires a combination of clinical, endocrinological, and genetic evaluation. The techniques used are described, with equal importance being given to each of the 3 approaches. Clinical skills are essential to elicit an accurate history, family pedigree, and symptoms of body system dysfunction. Endocrine assessment requires hormonal determination for the diagnosis of hormone deficiency and initiation of successful replacement therapy. Genetic analysis has added a new dimension to the investigation of short stature and now uses next-generation sequencing with a candidate gene approach to confirm probable recognizable monogenic disorders and exome sequencing for complex phenotypes of unknown origin. Using the 3 approaches of clinical, endocrine, and genetic probes with equal status in the hierarchy of investigational variables provides the clinician with the highest chance of identifying the correct causative pathogenetic mechanism in a child presenting with short stature of unknown origin.

Environmental DNA reveals arboreal cityscapes at the Ancient Maya Center of Tikal

Tikal, a major city of the ancient Maya world, has been the focus of archaeological research for over a century, yet the interactions between the Maya and the surrounding Neotropical forests remain largely enigmatic. This study aimed to help fill that void by using a powerful new technology, environmental DNA analysis, that enabled us to characterize the site core vegetation growing in association with the artificial reservoirs that provided the city water supply. Because the area has no permanent water sources, such as lakes or rivers, these reservoirs were key to the survival of the city, especially during the population expansion of the Classic period (250–850 CE). In the absence of specific evidence, the nature of the vegetation surrounding the reservoirs has been the subject of scientific hypotheses and artistic renderings for decades. To address these hypotheses we captured homologous sequences of vascular plant DNA extracted from reservoir sediments by using a targeted enrichment approach involving 120-bp genetic probes. Our samples encompassed the time before, during and after the occupation of Tikal (1000 BCE–900 CE). Results indicate that the banks of the ancient reservoirs were primarily fringed with native tropical forest vegetation rather than domesticated species during the Maya occupation.

Environmental DNA Reveals Arboreal Cityscapes at the Ancient Maya Center of Tikal

The city of Tikal, a major center of the ancient Maya world, has been the focus of archaeological research for over a century, yet the interactions between the Maya and the surrounding Neotropical forests remain largely enigmatic. To help fill that void, our study used a powerful new technology, environmental DNA analysis, which enabled us to characterize the site core vegetation associated with the artificial reservoirs that served as the city water supply. Because the area has no permanent water sources, these reservoirs were key to the survival of the city. In the absence of specific evidence, the nature of the vegetation surrounding the reservoirs has been the subject of scientific hypotheses for decades. To address these hypotheses we proceeded to capture homologous sequences of vascular plant DNA extracted from reservoir sediments using 120-bp genetic probes in a targeted enrichment approach. Samples date from the Early Preclassic period (1780 − 1620 BCE) to the Early Postclassic period (900–1100 CE), encompassing the time before, during and after the occupation of Tikal (1000 BCE-900 CE). Results indicate that during the Maya occupation the banks of the ancient reservoirs were primarily fringed with native tropical forest vegetation rather than domesticated species.

Presence of SARS-CoV-2 RNA in Semen—Cohort Study in the United States COVID-19 Positive Patients

On 31 December 2019, China informed the World Health Organization they were facing a viral pneumonia epidemic of a new type of Coronavirus. Currently, 10 months later, more than 43,000,000 people have been infected, and about 1,150,000 deceased worldwide from the disease. Knowledge about the virus is updated daily, and its RNA was isolated from several human secretions, e.g., throat, saliva, pulmonary alveolar washing, and feces. So far, only one publication found the presence of SARS-CoV-2 in semen. In this 5-month cross-sectional study, we recruited 15 patients diagnosed with a positive nasal swab for SARS-CoV-2 with no or mild symptoms in our institution. A semen sample after a shower was retrieved and tested for viral RNA in the semen. The samples were tested for the viral RNA with RT-PCR with two different genetic probes. The samples were re-tested 24 h after the first test to confirm the results. The SARS-Cov-2 viral RNA was present in 1/15 patients [6.66%] in our sample. Even in a small sample, the RNA from SARS-CoV-2 can be isolated from human semen. This information should alert the scientific community and public health officials about a possible new form of transmission of the disease and long-term clinical effects on the population.

DNA Methylation Profiles and Their Diagnostic Utility in BC

Biomarkers, including DNA methylation, have shown a great potential for use in personalized medicine for BC and especially for the diagnosis of BC in developing countries. According to the bisulfite sequencing PCR in twelve specimens (BC and matched normal tissues), nine genetic probes were designed to detect the frequency of methylation of the promoters in a total of 302 paired cases of BC and matched normal breast tissues. Finally, a total of 900 serum samples were used to validate the use of these methylation biomarkers for clinical diagnosis of BC. A high frequency of promoter methylation of SFN, HOXA11, P16, RARβ, PCDHGB7, hMLH1, WNT5a, HOXD13, and RASSF1a was observed in BC tissues. The methylation frequencies of HOXD13 and hMLH1 increased with the progression of BC. The methylation frequencies of HOXD13 and WNT5a were significantly higher in BC. We found that methylation modification-positive samples were most consistently associated with luminal BC. Finally, we confirmed that RASSF1a, P16, and PCDHGB7 displayed a significant sensitivity and specificity as diagnostic biomarkers for BC (P<0.001), and a panel that combined these three genes displayed increased significance (AUC, 0.781; P<0.001). These data suggest that epigenetic markers in serum can potentially be used to diagnose BC. The identification of additional BC-specific methylated genes would improve the sensitivity and specificity of this approach. This study could also indicate that different molecular subtypes of BC are caused by distinct genetic and epigenetic mechanisms.

The bioactive lipid (S)-sebastenoic acid impacts motility and dispersion in Vibrio cholerae

Although Gram-negative bacterial pathogens continue to impart a substantial burden on global healthcare systems, much remains to be understood about aspects of basic physiology in these organisms. In recent years, cyclic-diguanylate (c-di-GMP) has emerged as a key regulator of a number of important processes related to pathogenicity, including biofilm formation, motility, and virulence. In an effort to discover chemical genetic probes for studying Vibrio cholerae we have developed a new motility-based high-throughput screen to identify compounds that modulate c-di-GMP levels. Using this new screening platform, we tested a library of microbially derived marine natural products extracts, leading to the discovery of the bioactive lipid (S)-sebastenoic acid. The evaluation of the effect of this new compound on bacterial motility, vpsL expression, and biofilm formation implied that (S)-sebastenoic acid may alter phenotypes associated to c-di-GMP signaling in V. cholerae.