“The” genetic code?

The DNA‐based code for protein through messenger and transfer RNA is widely regarded as the code of life. But genomes are littered with other kinds of coding elements as well, and all of them probably came after a supercode for the tRNA system itself.     

而今迈步从头越: 马铃薯育种跨入“有种”时代

现代栽培马铃薯(Solanum tuberosum)是同源四倍体, 基因组高度杂合, 遗传组成复杂, 存在严重的自交衰退, 优异性状难以聚合, 使得育种周期漫长, 造成基于种子传代的马铃薯杂交育种难以突破。与此同时, 块茎无性繁殖导致马铃薯繁殖系数低、储运成本高和易携带病虫害等痼疾, 且种薯脱毒成本高, 限制其产业化发展。近期, 中国农业科学院深圳农业基因组研究所黄三文团队运用基因组设计理论和方法体系培育杂交马铃薯, 用二倍体育种替代四倍体育种, 实现了用杂交种子繁殖替代薯块繁殖, 创制了第1代高纯度的二倍体自交系和杂种优势明显的杂交马铃薯品系。该研究是马铃薯育种领域里程碑式的重大成果, 开启了基于基因组设计和种子迭代的马铃薯生物育种新纪元。     

“Where do I even start?” Recommendations for faculty diversifying syllabi in ecology,evolution, and the life sciences

Diversifying curricula is of increasing interest in higher education, including in ecology and evolution and allied fields. Yet, many educators may not know where to start. Here we provide a framework for meeting standard curriculum goals while enacting anti‐racist and anti‐colonial syllabi that is grounded in the development of a sustainable network of educators. In addition to highlighting this professional learning process and sharing the list of resources our group has developed, we provide suggestions to help educators highlight contributions of minoritized groups, explore multiple ways of knowing, and perform critical assessments of foundational views of life and environmental science fields. We further discuss the key classroom dynamics that affect the success of such anti‐racist and anti‐colonial initiatives. The retention and success of minoritized students in ecology and evolution depends on whether we address injustices in our fields. Our hope is that our fellow educators will use this paper to catalyze their own efforts to diversify their courses.     

“Rule of Six”: How Does the Sendai Virus RNA Polymerase Keep Count?

The "rule of six" stipulates that the Paramyxovirus RNA polymerase efficiently replicates only viral genomes counting 6n + 0 nucleotides. Because the nucleocapsid proteins (N) interact with 6 nucleotides, an exact nucleotide-N match at the RNA 3'-OH end (3'-OH congruence) may be required for recognition of an active replication promoter. Alternatively, assuming that the six positions for the interaction of N with the nucleotides are not equivalent, the nucleotide position relative to N may be critical (N phase context). The replication abilities of various minireplicons, designed so that the 3'-OH congruence could be discriminated from the N phase context, were studied. The results strongly suggest that the application of the rule of six depends on the recognition of nucleotides positioned in the proper N phase context.     

Elacestrant in metastatic breast cancer: Is the “standard of care” meeting standard requirements?

The EMERALD trial was an open label phase 3 trial evaluating elacestrant, the first oral selective estrogen receptor degrader (SERD), as compared to “standard of care”, in ER+/HER2- (hormone receptor positive, no HER2 overexpression) advanced or metastatic breast cancer.The EMERALD trial restricted the “standard of care” control arm to limited options that may have led to a substandard control arm. We describe how the EMERALD trial protocol allowed different clinically inappropriate scenarios in the control arm, according to prior therapy. The main relevant question remains the potential advantage of elacestrant over fulvestrant in fulvestrant-naive patients.Analyzing outcomes in subgroups according to prior and per-protocol therapy would help analyzing trial results. However, these subgroup results may be non-significant, and another randomized trial will be needed. Trials should be designed to answer directly clinical questions that are relevant.     

Local Recurrence of Soft Tissue Sarcoma Revisited: Is there a Role for “Selective” Radiation?

BackgroundRadiation therapy (RT) is often utilized in cases of high-grade soft tissue sarcoma (STS), but there remain situations where treatment is with surgical excision alone. Our goals were to determine (1) the local recurrence (LR) rate with and without perioperative RT and (2) associations between local recurrence, patient, tumor, and treatment variables.MethodsWe performed a retrospective review of 165 consecutive STS patients. A Cox proportional hazards model was used to investigate variables associated with local recurrence.ResultsLR occurred in 15/78 (19%) without RT, 4/29 (14%) with postoperative RT, and 0/58 with preoperative RT (p=0.002). We found increased rates of local recurrence at 24 months for myxofibrosarcoma (p=0.001) and no-RT (p=0.003). Myxofibrosarcoma accounted for 33 (20%) of the study patients and 12 (63%) of the local recurrences.ConclusionThe LR rate in patients treated with surgery alone was disproportionately attributable to myxofibrosarcoma (11/23 cases, 48%). Other subtypes demonstrated a lower rate of LR in the absence of RT (4/55 cases, 7%), and no LR occurred when final margins were >2 mm. In certain circumstances treatment with a negative margin surgical resection followed by close observation is justifiable. RT is effective and should continue to be considered routinely in myxofibrosarcoma or when surgical margins are inadequate. Level of Evidence: III     

Does “supersaturated coexistence” resolve the “paradox of the plankton”?

In contradiction with field observations, theory predicts that the number of coexisting plankton species at equilibrium cannot exceed the number of limiting resources, which is called the "paradox of the plankton". Recently, Huisman & Weissing (1999 , 2000 ) showed, in a model study, that the number of coexisting species may exceed the number of limiting resources when internal system feedback induces oscillations or chaos. In this paper, we use the term "supersaturated coexistence" for this phenomenon. On the basis of these findings, they claimed that the paradox of the plankton is solved. We investigated the prerequisites for supersaturated coexistence in the same model. Our results indicate that supersaturated coexistence is a rare phenomenon in parameter space, requires a very precise parameterization of the community members and is sensitive to the introduction of new species and the removal of the present species. This raises the question of whether supersaturated coexistence is likely to occur in nature. We conclude that the claim by Huisman & Weissing (1999 , 2000 ) is premature.     

“Ryanopathies” and RyR2 dysfunctions: can we further decipher them using in vitro human disease models?

The regulation of intracellular calcium (Ca²⁺) homeostasis is fundamental to maintain normal functions in many cell types. The ryanodine receptor (RyR), the largest intracellular calcium release channel located on the sarco/endoplasmic reticulum (SR/ER), plays a key role in the intracellular Ca²⁺ handling. Abnormal type 2 ryanodine receptor (RyR2) function, associated to mutations (ryanopathies) or pathological remodeling, has been reported, not only in cardiac diseases, but also in neuronal and pancreatic disorders. While animal models and in vitro studies provided valuable contributions to our knowledge on RyR2 dysfunctions, the human cell models derived from patients’ cells offer new hope for improving our understanding of human clinical diseases and enrich the development of great medical advances. We here discuss the current knowledge on RyR2 dysfunctions associated with mutations and post-translational remodeling. We then reviewed the novel human cellular technologies allowing the correlation of patient’s genome with their cellular environment and providing approaches for personalized RyR-targeted therapeutics.Subject terms: Ventricular tachycardia, Ventricular tachycardia     

Revisiting “what do tadpoles really eat?” A 10‐year perspective

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Can paleopathology provide evidence for “compassion”?

Paleopathological analyses of skeletal remains have provided significant information about diet and health in prehistoric populations. A number of individuals have been recovered whose remains show evidence of impairments that would have precluded "normal" functioning, resulting in a disability. The most famous example is Shanidar I; more recent discoveries include the Romito 2 dwarf from Italy and a boy with spina bifida from the Windover site in Florida. These finds have been interpreted by some writers as evidence for compassion and "moral decency" among the other members of the community, who would have had to support these nonproductive individuals. However, these interpretations are based on a number of implicit assumptions: about the number of nonproductive members normally present in any population, about the abilities of disabled individuals to contribute to society, about the treatment of disabled individuals by other members of the group, and about the "moral rightness" of facilitating the survival of a disabled individual under all circumstances. These assumptions are not justified by the evidence from the archeological record or by reference to ethnographic analogy. A tendency to focus on physical traits as the sole measure of productive ability, images of Rousseau's "noble savage" transported to the past, and unexamined beliefs about the disabled in modern societies have influenced these archeological interpretations. We are not justified in drawing conclusions either about the quality of life for disabled individuals in the past or about the motives or attitudes of the rest of the community from skeletal evidence of physical impairment.     

Are the Kow Swamp hominids “archaic”?

Initial reports of hominids recovered at Kow Swamp, in the Murray Valley of Victoria indicated that, on the basis of cranial analyses, there was a "survival of Homo erectus features in Australia until as recently as 10,000 years ago (Thorne and Macumber, 1972, p. 316). This claim was later refuted by others, who suggested that artificial cranial deformation may have been responsible for at least some of the distinctive and "primitive" traits seen in the Kow Swamp individuals. Previous research by this worker and others has indicated that taxonomic traits at both specific and subspecific levels are present in hominine femora. Therefore, it may be possible to evaluate the "primitiveness" of the Kow Swamp sample on the basis of their femoral anatomy. Morphometric analyses were undertaken, using as controls femora of Romano British, Tasmanian, and other Murray Valley populations. On the basis of bivariate and multivariate analyses it was found that, at least in this single element of the postcranium, no primitive features were present. The Kow Swamp sample, in fact, shows a very close morphometric relationship with all included Homo sapiens controls and is significantly distinct from Homo erectus.